6-31273182-C-G

Variant names:

• chr6-31273182-C-G
• rs7773175

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 0.264 in 151,792 control chromosomes in the GnomAD database, including 5,440 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 0.26 (5440 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 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: 0.264 AC: 39996 AN: 151672 Hom.: 5438 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.264 AC: 39999 AN: 151792 Hom.: 5440 Cov.: 31 AF XY: 0.260 AC XY: 19317 AN XY: 74192

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.278

Alfa AF: 0.0763 Hom.: 91

Bravo AF: 0.266

Asia WGS AF: 0.268 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.048
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7773175; hg19: chr6-31240959;