rs79842896

Variant names:

• chr7-55276481-T-C
• rs79842896

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0273 in 152,256 control chromosomes in the GnomAD database, including 93 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 0.027 (93 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0273 (4162/152256) while in subpopulation NFE AF = 0.0422 (2869/68012). AF 95% confidence interval is 0.0409. There are 93 homozygotes in GnomAd4. There are 1985 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 93 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: 0.0274 AC: 4163 AN: 152138 Hom.: 93 Cov.: 33

Gnomad AFR AF: 0.00642

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0249

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0266

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0422

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0273 AC: 4162 AN: 152256 Hom.: 93 Cov.: 33 AF XY: 0.0267 AC XY: 1985 AN XY: 74460

African (AFR) AF: 0.00640 AC: 266 AN: 41560

American (AMR) AF: 0.0248 AC: 380 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0695 AC: 241 AN: 3470

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5166

South Asian (SAS) AF: 0.0266 AC: 128 AN: 4812

European-Finnish (FIN) AF: 0.0199 AC: 211 AN: 10614

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0422 AC: 2869 AN: 68012

Other (OTH) AF: 0.0237 AC: 50 AN: 2108

Alfa AF: 0.0350 Hom.: 16

Bravo AF: 0.0270

Asia WGS AF: 0.0100 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.81
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs79842896; hg19: chr7-55344174;