chr7-74079203-A-G

Variant names:

• chr7-74079203-A-G
• rs810549

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 0.163 in 152,156 control chromosomes in the GnomAD database, including 2,422 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 0.16 (2422 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 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: 0.163 AC: 24783 AN: 152038 Hom.: 2409 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.163 AC: 24813 AN: 152156 Hom.: 2422 Cov.: 32 AF XY: 0.165 AC XY: 12293 AN XY: 74382

African (AFR) AF: 0.0699 AC: 2905 AN: 41534

American (AMR) AF: 0.250 AC: 3819 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3466

East Asian (EAS) AF: 0.268 AC: 1390 AN: 5180

South Asian (SAS) AF: 0.126 AC: 607 AN: 4824

European-Finnish (FIN) AF: 0.166 AC: 1759 AN: 10584

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12710 AN: 67988

Other (OTH) AF: 0.218 AC: 459 AN: 2106

Alfa AF: 0.178 Hom.: 3992

Bravo AF: 0.167

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.77
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs810549; hg19: chr7-73493533;