3-77700277-T-C

Position:

• chr3-77700277-T-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 0.211 in 151,546 control chromosomes in the GnomAD database, including 3,590 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 0.21 (3590 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32005 AN: 151426 Hom.: 3587 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.211 AC: 32022 AN: 151546 Hom.: 3590 Cov.: 31 AF XY: 0.212 AC XY: 15690 AN XY: 74036

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.234

Alfa AF: 0.235 Hom.: 8958

Bravo AF: 0.202

Asia WGS AF: 0.340 AC: 1184 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1669215; hg19: chr3-77749428;