3-77700277-T-C

Variant names:

• chr3-77700277-T-C
• rs1669215

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.144 AC: 5940 AN: 41334

American (AMR) AF: 0.185 AC: 2813 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3470

East Asian (EAS) AF: 0.383 AC: 1962 AN: 5120

South Asian (SAS) AF: 0.296 AC: 1415 AN: 4784

European-Finnish (FIN) AF: 0.204 AC: 2138 AN: 10470

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16031 AN: 67864

Other (OTH) AF: 0.234 AC: 492 AN: 2102

Alfa AF: 0.231 Hom.: 18131

Bravo AF: 0.202

Asia WGS AF: 0.340 AC: 1184 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.66
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1669215; hg19: chr3-77749428;