rs273098

Variant names:

• chr7-41386301-A-C
• rs273098

Your query was ambiguous. Multiple possible variants found:

• chr7-41386301-A-C
• chr7-41386301-A-G
• chr7-41386301-A-T

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 0.653 in 151,790 control chromosomes in the GnomAD database, including 33,199 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 0.65 (33199 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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: 0.652 AC: 98952 AN: 151672 Hom.: 33148 Cov.: 30

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.653 AC: 99062 AN: 151790 Hom.: 33199 Cov.: 30 AF XY: 0.650 AC XY: 48213 AN XY: 74144

African (AFR) AF: 0.821 AC: 33968 AN: 41384

American (AMR) AF: 0.669 AC: 10212 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1970 AN: 3460

East Asian (EAS) AF: 0.496 AC: 2548 AN: 5134

South Asian (SAS) AF: 0.569 AC: 2734 AN: 4804

European-Finnish (FIN) AF: 0.551 AC: 5787 AN: 10512

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.585 AC: 39752 AN: 67920

Other (OTH) AF: 0.640 AC: 1347 AN: 2106

Alfa AF: 0.482 Hom.: 1335

Bravo AF: 0.670

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.53
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs273098; hg19: chr7-41425899;