rs6789153

Variant names:

• chr3-70952104-C-G
• rs6789153

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 0.172 in 152,174 control chromosomes in the GnomAD database, including 5,843 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 0.17 (5843 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 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: 0.172 AC: 26111 AN: 152056 Hom.: 5819 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0636

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.172 AC: 26178 AN: 152174 Hom.: 5843 Cov.: 32 AF XY: 0.171 AC XY: 12731 AN XY: 74414

African (AFR) AF: 0.506 AC: 20967 AN: 41466

American (AMR) AF: 0.0633 AC: 969 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2004 AN: 5168

South Asian (SAS) AF: 0.118 AC: 571 AN: 4830

European-Finnish (FIN) AF: 0.0277 AC: 294 AN: 10610

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0132 AC: 900 AN: 68024

Other (OTH) AF: 0.142 AC: 299 AN: 2102

Alfa AF: 0.109 Hom.: 424

Bravo AF: 0.192

Asia WGS AF: 0.283 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.63
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6789153; hg19: chr3-71001255;