rs1722601

Positions:

• chr7-63474056-G-A
• chr7-63474056-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.588 in 151,396 control chromosomes in the GnomAD database, including 27,048 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 0.59 (27048 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

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: 0.587 AC: 88863 AN: 151278 Hom.: 26985 Cov.: 30

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.588 AC: 88987 AN: 151396 Hom.: 27048 Cov.: 30 AF XY: 0.596 AC XY: 44116 AN XY: 73960

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.575

Alfa AF: 0.537 Hom.: 2790

Bravo AF: 0.599

Asia WGS AF: 0.732 AC: 2544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1722601; hg19: chr7-62934434;