chr6-25895347-T-C

Variant names:

• chr6-25895347-T-C
• rs6910741

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 0.174 in 152,126 control chromosomes in the GnomAD database, including 3,128 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 (3128 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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: 0.174 AC: 26482 AN: 152008 Hom.: 3122 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.174 AC: 26497 AN: 152126 Hom.: 3128 Cov.: 31 AF XY: 0.182 AC XY: 13503 AN XY: 74380

African (AFR) AF: 0.111 AC: 4603 AN: 41488

American (AMR) AF: 0.266 AC: 4064 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 689 AN: 3472

East Asian (EAS) AF: 0.621 AC: 3205 AN: 5164

South Asian (SAS) AF: 0.287 AC: 1383 AN: 4822

European-Finnish (FIN) AF: 0.149 AC: 1577 AN: 10594

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10394 AN: 67984

Other (OTH) AF: 0.217 AC: 459 AN: 2114

Alfa AF: 0.168 Hom.: 4935

Bravo AF: 0.182

Asia WGS AF: 0.400 AC: 1385 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs6910741; hg19: chr6-25895575;