rs7773175

Positions:

• chr6-31273182-C-G
• chr6-31273182-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;