rs2615913

chr11-33460412-T-Achr11-33460412-T-Cchr11-33460412-T-G

Variant summary

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

The NM_012194.3(KIAA1549L):c.239-81390T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,932 control chromosomes in the GnomAD database, including 32,386 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 0.64 (32386 hom., cov: 31)
• Consequence: KIAA1549L NM_012194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

Genes affected

KIAA1549L (HGNC:24836): (KIAA1549 like) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1549L	NM_012194.3	c.239-81390T>A		intron_variant		ENST00000658780.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1549L	ENST00000658780.2	c.239-81390T>A		intron_variant			NM_012194.3	P2
KIAA1549L	ENST00000526400.7	c.239-81390T>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97644 AN: 151814 Hom.: 32351 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.643 AC: 97731 AN: 151932 Hom.: 32386 Cov.: 31 AF XY: 0.641 AC XY: 47614 AN XY: 74276

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.613

Alfa AF: 0.604 Hom.: 3366

Bravo AF: 0.650

Asia WGS AF: 0.604 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.56
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2615913; hg19: chr11-33481958;