rs9976971

Positions:

• chr21-33395791-A-G
• chr21-33395791-A-T

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 0.659 in 151,980 control chromosomes in the GnomAD database, including 34,565 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 0.66 (34565 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 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: 0.658 AC: 99996 AN: 151862 Hom.: 34509 Cov.: 30

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.659 AC: 100103 AN: 151980 Hom.: 34565 Cov.: 30 AF XY: 0.655 AC XY: 48681 AN XY: 74286

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.643

Alfa AF: 0.580 Hom.: 33748

Bravo AF: 0.670

Asia WGS AF: 0.671 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.61
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9976971; hg19: chr21-34768097;