rs10954631

Positions:

• chr7-138854880-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001164665.2(KIAA1549):​c.5248-2611C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,070 control chromosomes in the GnomAD database, including 12,049 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 0.27 (12049 hom., cov: 32)
• Consequence: KIAA1549 NM_001164665.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1549	NM_001164665.2	c.5248-2611C>T		intron_variant		ENST00000422774.2	NP_001158137.1
KIAA1549	NM_020910.3	c.5248-2611C>T		intron_variant			NP_065961.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1549	ENST00000422774.2	c.5248-2611C>T		intron_variant		1	NM_001164665.2	ENSP00000416040	A2
KIAA1549	ENST00000440172.5	c.5248-2611C>T		intron_variant		1		ENSP00000406661	P4

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41160 AN: 151952 Hom.: 11998 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.246

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.271 AC: 41266 AN: 152070 Hom.: 12049 Cov.: 32 AF XY: 0.265 AC XY: 19737 AN XY: 74358

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.0747

Gnomad4 OTH AF: 0.247

Alfa AF: 0.107 Hom.: 2718

Bravo AF: 0.298

Asia WGS AF: 0.190 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs10954631; hg19: chr7-138539626; COSMIC: COSV99650617;