6-31238429-C-T

Position:

• chr6-31238429-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 0.492 in 151,918 control chromosomes in the GnomAD database, including 18,491 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 0.49 (18491 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31238429C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74742 AN: 151800 Hom.: 18468 Cov.: 31

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.492 AC: 74805 AN: 151918 Hom.: 18491 Cov.: 31 AF XY: 0.492 AC XY: 36575 AN XY: 74270

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.529

Alfa AF: 0.454 Hom.: 17161

Bravo AF: 0.493

Asia WGS AF: 0.551 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130685; hg19: chr6-31206206;