rs6788217

Variant names:

• chr3-1675155-A-C
• rs6788217

Your query was ambiguous. Multiple possible variants found:

• chr3-1675155-A-C
• chr3-1675155-A-T

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 0.297 in 151,934 control chromosomes in the GnomAD database, including 7,224 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 0.30 (7224 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 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: 0.297 AC: 45027 AN: 151820 Hom.: 7212 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.297 AC: 45070 AN: 151934 Hom.: 7224 Cov.: 32 AF XY: 0.298 AC XY: 22132 AN XY: 74278

African (AFR) AF: 0.321 AC: 13317 AN: 41436

American (AMR) AF: 0.270 AC: 4112 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3468

East Asian (EAS) AF: 0.646 AC: 3330 AN: 5152

South Asian (SAS) AF: 0.262 AC: 1263 AN: 4814

European-Finnish (FIN) AF: 0.322 AC: 3408 AN: 10572

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17726 AN: 67956

Other (OTH) AF: 0.299 AC: 630 AN: 2108

Alfa AF: 0.236 Hom.: 1474

Bravo AF: 0.297

Asia WGS AF: 0.431 AC: 1494 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.58
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs6788217; hg19: chr3-1716839;