chr3-8971219-T-C

Variant names:

• chr3-8971219-T-C
• rs369651

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 0.59 in 152,168 control chromosomes in the GnomAD database, including 28,492 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 (28492 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.714 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: 0.590 AC: 89729 AN: 152050 Hom.: 28491 Cov.: 34

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.590 AC: 89750 AN: 152168 Hom.: 28492 Cov.: 34 AF XY: 0.595 AC XY: 44259 AN XY: 74400

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.625

Alfa AF: 0.672 Hom.: 56102

Bravo AF: 0.576

Asia WGS AF: 0.533 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs369651; hg19: chr3-9012903;