rs79842896

Positions:

• chr7-55276481-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 93 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00640

Gnomad4 AMR AF: 0.0248

Gnomad4 ASJ AF: 0.0695

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0266

Gnomad4 FIN AF: 0.0199

Gnomad4 NFE AF: 0.0422

Gnomad4 OTH AF: 0.0237

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79842896; hg19: chr7-55344174;