3-89975872-C-T

Variant names:

• chr3-89975872-C-T
• rs6776967

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 0.193 in 151,928 control chromosomes in the GnomAD database, including 3,161 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 0.19 (3161 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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: 0.193 AC: 29246 AN: 151810 Hom.: 3164 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0958

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.193 AC: 29251 AN: 151928 Hom.: 3161 Cov.: 32 AF XY: 0.191 AC XY: 14185 AN XY: 74218

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.0958

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0813

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.151

Alfa AF: 0.217 Hom.: 7365

Bravo AF: 0.182

Asia WGS AF: 0.110 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.37
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6776967; hg19: chr3-90025022;