6-71772755-C-T

Variant names:

• chr6-71772755-C-T
• rs10455248

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.254

Alfa AF: 0.262 Hom.: 8281

Bravo AF: 0.227

Asia WGS AF: 0.141 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10455248; hg19: chr6-72482458;