rs7802273

Variant names:

• chr7-49649194-A-G
• rs7802273

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 0.579 in 151,998 control chromosomes in the GnomAD database, including 26,538 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 0.58 (26538 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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: 0.579 AC: 87969 AN: 151878 Hom.: 26517 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.579 AC: 88043 AN: 151998 Hom.: 26538 Cov.: 32 AF XY: 0.583 AC XY: 43311 AN XY: 74296

African (AFR) AF: 0.744 AC: 30863 AN: 41456

American (AMR) AF: 0.534 AC: 8154 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3470

East Asian (EAS) AF: 0.776 AC: 4011 AN: 5168

South Asian (SAS) AF: 0.523 AC: 2522 AN: 4826

European-Finnish (FIN) AF: 0.527 AC: 5555 AN: 10550

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33292 AN: 67946

Other (OTH) AF: 0.582 AC: 1230 AN: 2112

Alfa AF: 0.514 Hom.: 10430

Bravo AF: 0.591

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.48
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs7802273; hg19: chr7-49688790;