rs404909

Variant names:

• chr7-159193053-C-T
• rs404909

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 0.635 in 152,228 control chromosomes in the GnomAD database, including 32,125 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 (32125 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 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: 0.635 AC: 96662 AN: 152108 Hom.: 32110 Cov.: 35

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.635 AC: 96703 AN: 152228 Hom.: 32125 Cov.: 35 AF XY: 0.623 AC XY: 46380 AN XY: 74414

African (AFR) AF: 0.484 AC: 20121 AN: 41542

American (AMR) AF: 0.612 AC: 9361 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2582 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1545 AN: 5176

South Asian (SAS) AF: 0.600 AC: 2898 AN: 4826

European-Finnish (FIN) AF: 0.597 AC: 6316 AN: 10576

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51539 AN: 68022

Other (OTH) AF: 0.670 AC: 1416 AN: 2114

Alfa AF: 0.686 Hom.: 4565

Bravo AF: 0.629

Asia WGS AF: 0.431 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.44
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs404909; hg19: chr7-158985743;