rs854571

Variant names:

• chr7-95325307-T-C
• rs854571

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 0.624 in 152,038 control chromosomes in the GnomAD database, including 30,952 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 0.62 (30952 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 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: 0.624 AC: 94841 AN: 151922 Hom.: 30934 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.624 AC: 94900 AN: 152038 Hom.: 30952 Cov.: 32 AF XY: 0.628 AC XY: 46697 AN XY: 74348

African (AFR) AF: 0.416 AC: 17264 AN: 41456

American (AMR) AF: 0.673 AC: 10285 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2652 AN: 3466

East Asian (EAS) AF: 0.707 AC: 3646 AN: 5158

South Asian (SAS) AF: 0.610 AC: 2940 AN: 4820

European-Finnish (FIN) AF: 0.710 AC: 7505 AN: 10564

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48257 AN: 67972

Other (OTH) AF: 0.680 AC: 1435 AN: 2110

Alfa AF: 0.686 Hom.: 110985

Bravo AF: 0.615

Asia WGS AF: 0.664 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.40
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs854571; hg19: chr7-94954619;