chr7-138833311-C-T

Variant names:

• chr7-138833311-C-T
• rs896193
• NM_001164665.2:c.*4595G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001164665.2(KIAA1549):​c.*4595G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 232,280 control chromosomes in the GnomAD database, including 72,311 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.79 (48117 hom., cov: 33)
  • Exomes 𝑓: 0.77 (24194 hom.)
• Consequence: KIAA1549 NM_001164665.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.914
• Publications: 3 publications found

Genes affected

KIAA1549 (HGNC:22219): (KIAA1549) The protein encoded by this gene belongs to the UPF0606 family. This gene has been found to be fused to the BRAF oncogene in many cases of pilocytic astrocytoma. The fusion results from 2Mb tandem duplications at 7q34. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2012]

TMEM213 (HGNC:27220): (transmembrane protein 213) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164665.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1549	NM_001164665.2	MANE Select	c.*4595G>A		3_prime_UTR	Exon 20 of 20	NP_001158137.1
	KIAA1549	NM_020910.3		c.*4595G>A		3_prime_UTR	Exon 20 of 20	NP_065961.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1549	ENST00000422774.2	TSL:1 MANE Select	c.*4595G>A		3_prime_UTR	Exon 20 of 20	ENSP00000416040.2
	KIAA1549	ENST00000440172.5	TSL:1	c.*4595G>A		3_prime_UTR	Exon 20 of 20	ENSP00000406661.1
	TMEM213	ENST00000413208.1	TSL:3	c.155-4558C>T		intron	N/A	ENSP00000401570.1

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119629 AN: 152064 Hom.: 48051 Cov.: 33

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.797

GnomAD4 exome AF: 0.773 AC: 61899 AN: 80098 Hom.: 24194 Cov.: 0 AF XY: 0.772 AC XY: 28481 AN XY: 36878

African (AFR) AF: 0.953 AC: 3670 AN: 3852

American (AMR) AF: 0.712 AC: 1759 AN: 2470

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 3927 AN: 5078

East Asian (EAS) AF: 0.954 AC: 10768 AN: 11286

South Asian (SAS) AF: 0.669 AC: 463 AN: 692

European-Finnish (FIN) AF: 0.700 AC: 42 AN: 60

Middle Eastern (MID) AF: 0.808 AC: 396 AN: 490

European-Non Finnish (NFE) AF: 0.723 AC: 35780 AN: 49496

Other (OTH) AF: 0.763 AC: 5094 AN: 6674

GnomAD4 genome AF: 0.787 AC: 119756 AN: 152182 Hom.: 48117 Cov.: 33 AF XY: 0.782 AC XY: 58155 AN XY: 74378

African (AFR) AF: 0.950 AC: 39473 AN: 41538

American (AMR) AF: 0.713 AC: 10898 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2677 AN: 3472

East Asian (EAS) AF: 0.912 AC: 4732 AN: 5186

South Asian (SAS) AF: 0.687 AC: 3310 AN: 4816

European-Finnish (FIN) AF: 0.660 AC: 6978 AN: 10576

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49079 AN: 67992

Other (OTH) AF: 0.799 AC: 1687 AN: 2112

Alfa AF: 0.741 Hom.: 69826

Bravo AF: 0.805

Asia WGS AF: 0.826 AC: 2872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.71
PhyloP100		0.91
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs896193; hg19: chr7-138518056;