chr7-21960807-G-A

Position:

• chr7-21960807-G-A

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 0.561 in 148,918 control chromosomes in the GnomAD database, including 23,719 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 0.56 (23719 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.971

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 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: 0.561 AC: 83421 AN: 148800 Hom.: 23712 Cov.: 24

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.561 AC: 83469 AN: 148918 Hom.: 23719 Cov.: 24 AF XY: 0.562 AC XY: 40630 AN XY: 72344

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.538

Alfa AF: 0.546 Hom.: 46112

Bravo AF: 0.562

Asia WGS AF: 0.426 AC: 1487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6461625; hg19: chr7-22000425;