rs6796720

Variant names:

• chr3-109888085-C-T
• rs6796720

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 0.207 in 152,040 control chromosomes in the GnomAD database, including 3,564 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 (3564 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.207 AC: 31509 AN: 151922 Hom.: 3561 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.0687

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.207 AC: 31522 AN: 152040 Hom.: 3564 Cov.: 32 AF XY: 0.202 AC XY: 15026 AN XY: 74304

African (AFR) AF: 0.293 AC: 12164 AN: 41450

American (AMR) AF: 0.138 AC: 2114 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3464

East Asian (EAS) AF: 0.0196 AC: 101 AN: 5164

South Asian (SAS) AF: 0.0682 AC: 329 AN: 4826

European-Finnish (FIN) AF: 0.215 AC: 2271 AN: 10580

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13197 AN: 67970

Other (OTH) AF: 0.198 AC: 417 AN: 2108

Alfa AF: 0.190 Hom.: 1690

Bravo AF: 0.206

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs6796720; hg19: chr3-109606932;