chr6-15664974-G-A

Variant names:

• chr6-15664974-G-A
• rs12204704

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 0.178 in 152,190 control chromosomes in the GnomAD database, including 2,517 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 0.18 (2517 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27051 AN: 152072 Hom.: 2513 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.178 AC: 27076 AN: 152190 Hom.: 2517 Cov.: 32 AF XY: 0.182 AC XY: 13538 AN XY: 74408

African (AFR) AF: 0.162 AC: 6716 AN: 41500

American (AMR) AF: 0.143 AC: 2189 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 946 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1459 AN: 5186

South Asian (SAS) AF: 0.322 AC: 1553 AN: 4820

European-Finnish (FIN) AF: 0.165 AC: 1750 AN: 10594

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11842 AN: 68004

Other (OTH) AF: 0.199 AC: 421 AN: 2112

Alfa AF: 0.177 Hom.: 505

Bravo AF: 0.170

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs12204704; hg19: chr6-15665205;