rs34401238

Variant names:

• chr7-99795295-C-CACA
• rs34401238

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The variant allele was found at a frequency of 0.0235 in 152,254 control chromosomes in the GnomAD database, including 69 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.024 (69 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0235 (3580/152254) while in subpopulation SAS AF = 0.0521 (251/4818). AF 95% confidence interval is 0.0468. There are 69 homozygotes in GnomAd4. There are 1783 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 69 gene

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: 0.0235 AC: 3578 AN: 152136 Hom.: 69 Cov.: 31

Gnomad AFR AF: 0.00444

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0235 AC: 3580 AN: 152254 Hom.: 69 Cov.: 31 AF XY: 0.0240 AC XY: 1783 AN XY: 74430

African (AFR) AF: 0.00443 AC: 184 AN: 41550

American (AMR) AF: 0.0240 AC: 367 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0521 AC: 251 AN: 4818

European-Finnish (FIN) AF: 0.0222 AC: 235 AN: 10594

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0339 AC: 2305 AN: 68024

Other (OTH) AF: 0.0284 AC: 60 AN: 2114

Alfa AF: 0.0287 Hom.: 4

Bravo AF: 0.0213

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs34401238; hg19: chr7-99392918;