6-71772755-C-T

Variant names:

• chr6-71772755-C-T
• rs10455248

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 0.23 in 151,996 control chromosomes in the GnomAD database, including 4,557 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 0.23 (4557 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 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: 0.230 AC: 34963 AN: 151878 Hom.: 4551 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.230 AC: 34979 AN: 151996 Hom.: 4557 Cov.: 32 AF XY: 0.230 AC XY: 17083 AN XY: 74308

African (AFR) AF: 0.125 AC: 5197 AN: 41458

American (AMR) AF: 0.282 AC: 4308 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 812 AN: 3458

East Asian (EAS) AF: 0.111 AC: 571 AN: 5164

South Asian (SAS) AF: 0.131 AC: 632 AN: 4814

European-Finnish (FIN) AF: 0.317 AC: 3344 AN: 10564

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19250 AN: 67946

Other (OTH) AF: 0.254 AC: 535 AN: 2106

Alfa AF: 0.260 Hom.: 17992

Bravo AF: 0.227

Asia WGS AF: 0.141 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.78
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs10455248; hg19: chr6-72482458;