6-22743174-A-G

Variant names:

• chr6-22743174-A-G
• rs10498712

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 0.3 in 151,866 control chromosomes in the GnomAD database, including 6,901 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 (6901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• Publications: 14 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 = 0.316 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: 0.300 AC: 45577 AN: 151748 Hom.: 6895 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.300 AC: 45587 AN: 151866 Hom.: 6901 Cov.: 32 AF XY: 0.299 AC XY: 22179 AN XY: 74212

African (AFR) AF: 0.321 AC: 13304 AN: 41462

American (AMR) AF: 0.188 AC: 2868 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3466

East Asian (EAS) AF: 0.252 AC: 1293 AN: 5128

South Asian (SAS) AF: 0.300 AC: 1449 AN: 4826

European-Finnish (FIN) AF: 0.343 AC: 3628 AN: 10570

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20968 AN: 67858

Other (OTH) AF: 0.281 AC: 592 AN: 2108

Alfa AF: 0.310 Hom.: 25927

Bravo AF: 0.288

Asia WGS AF: 0.294 AC: 1027 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.64
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs10498712; hg19: chr6-22743403;