chr6-15671500-T-C

Variant names:

• chr6-15671500-T-C
• rs2769563

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 0.143 in 152,286 control chromosomes in the GnomAD database, including 2,138 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 0.14 (2138 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.144 AC: 21838 AN: 152168 Hom.: 2142 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.0502

Gnomad FIN AF: 0.0699

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.143 AC: 21843 AN: 152286 Hom.: 2138 Cov.: 32 AF XY: 0.139 AC XY: 10354 AN XY: 74468

African (AFR) AF: 0.276 AC: 11464 AN: 41542

American (AMR) AF: 0.154 AC: 2357 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5194

South Asian (SAS) AF: 0.0509 AC: 246 AN: 4832

European-Finnish (FIN) AF: 0.0699 AC: 742 AN: 10610

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0939 AC: 6387 AN: 68024

Other (OTH) AF: 0.123 AC: 260 AN: 2110

Alfa AF: 0.111 Hom.: 1511

Bravo AF: 0.158

Asia WGS AF: 0.0350 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.62
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs2769563; hg19: chr6-15671731;