rs12641042

Variant names:

• chr4-74347621-C-A
• rs12641042
• ENST00000805841.1:n.192-17317G>T

Variant summary

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

The ENST00000805841.1(ENSG00000304732):​n.192-17317G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,742 control chromosomes in the GnomAD database, including 9,509 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 0.34 (9509 hom., cov: 31)
• Consequence: ENSG00000304732 ENST00000805841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 6 publications found

Genes affected

ENSG00000304732 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377276	NR_188415.1	n.192-17317G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304732	ENST00000805841.1	n.192-17317G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51837 AN: 151624 Hom.: 9486 Cov.: 31

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.342 AC: 51919 AN: 151742 Hom.: 9509 Cov.: 31 AF XY: 0.348 AC XY: 25775 AN XY: 74154

African (AFR) AF: 0.443 AC: 18324 AN: 41362

American (AMR) AF: 0.402 AC: 6123 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 945 AN: 3460

East Asian (EAS) AF: 0.466 AC: 2400 AN: 5152

South Asian (SAS) AF: 0.452 AC: 2174 AN: 4808

European-Finnish (FIN) AF: 0.295 AC: 3101 AN: 10524

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17902 AN: 67894

Other (OTH) AF: 0.312 AC: 657 AN: 2106

Alfa AF: 0.322 Hom.: 1390

Bravo AF: 0.354

Asia WGS AF: 0.473 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.54
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs12641042; hg19: chr4-75213338;