rs6003914

Variant names:

• chr22-23844450-T-C
• rs6003914

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 0.166 in 152,160 control chromosomes in the GnomAD database, including 2,660 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 (2660 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20
• Publications: 5 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 = 0.292 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: 0.166 AC: 25270 AN: 152042 Hom.: 2652 Cov.: 35

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0628

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.166 AC: 25318 AN: 152160 Hom.: 2660 Cov.: 35 AF XY: 0.168 AC XY: 12498 AN XY: 74392

African (AFR) AF: 0.296 AC: 12284 AN: 41480

American (AMR) AF: 0.112 AC: 1706 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0628 AC: 218 AN: 3470

East Asian (EAS) AF: 0.196 AC: 1013 AN: 5178

South Asian (SAS) AF: 0.165 AC: 795 AN: 4822

European-Finnish (FIN) AF: 0.204 AC: 2165 AN: 10596

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0999 AC: 6795 AN: 67992

Other (OTH) AF: 0.136 AC: 287 AN: 2116

Alfa AF: 0.120 Hom.: 363

Bravo AF: 0.166

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.37
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs6003914; hg19: chr22-24186637;