rs2615945

Variant names:

• chr11-33412077-G-A
• rs2615945
• NM_012194.3:c.238+35188G>A

Variant summary

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

The NM_012194.3(KIAA1549L):​c.238+35188G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,064 control chromosomes in the GnomAD database, including 9,528 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 0.35 (9528 hom., cov: 32)
• Consequence: KIAA1549L NM_012194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 4 publications found

Genes affected

KIAA1549L (HGNC:24836): (KIAA1549 like) 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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1549L	NM_012194.3	c.238+35188G>A		intron_variant	Intron 1 of 20	ENST00000658780.2	NP_036326.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1549L	ENST00000658780.2	c.238+35188G>A		intron_variant	Intron 1 of 20		NM_012194.3	ENSP00000499430.1
KIAA1549L	ENST00000526400.7	c.238+35188G>A		intron_variant	Intron 1 of 20	5		ENSP00000433481.3

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52609 AN: 151946 Hom.: 9513 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.346 AC: 52646 AN: 152064 Hom.: 9528 Cov.: 32 AF XY: 0.348 AC XY: 25878 AN XY: 74338

African (AFR) AF: 0.271 AC: 11261 AN: 41478

American (AMR) AF: 0.348 AC: 5318 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1258 AN: 3470

East Asian (EAS) AF: 0.116 AC: 602 AN: 5178

South Asian (SAS) AF: 0.304 AC: 1467 AN: 4820

European-Finnish (FIN) AF: 0.448 AC: 4736 AN: 10564

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26989 AN: 67952

Other (OTH) AF: 0.310 AC: 654 AN: 2110

Alfa AF: 0.376 Hom.: 46935

Bravo AF: 0.336

Asia WGS AF: 0.199 AC: 693 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.63
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2615945; hg19: chr11-33433623;