7-41402009-T-C

Variant names:

• chr7-41402009-T-C
• rs404569

Variant summary

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

The variant allele was found at a frequency of 0.653 in 151,934 control chromosomes in the GnomAD database, including 33,250 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 0.65 (33250 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99093 AN: 151816 Hom.: 33198 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.653 AC: 99203 AN: 151934 Hom.: 33250 Cov.: 32 AF XY: 0.650 AC XY: 48272 AN XY: 74224

African (AFR) AF: 0.820 AC: 34024 AN: 41482

American (AMR) AF: 0.669 AC: 10203 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1972 AN: 3468

East Asian (EAS) AF: 0.496 AC: 2567 AN: 5176

South Asian (SAS) AF: 0.580 AC: 2788 AN: 4810

European-Finnish (FIN) AF: 0.551 AC: 5794 AN: 10516

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39758 AN: 67912

Other (OTH) AF: 0.640 AC: 1352 AN: 2112

Alfa AF: 0.626 Hom.: 3970

Bravo AF: 0.670

Asia WGS AF: 0.576 AC: 2003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.45
DANN	Benign	0.16
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs404569; hg19: chr7-41441607;