6-31439866-T-C

Position:

• chr6-31439866-T-C

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 0.364 in 151,470 control chromosomes in the GnomAD database, including 10,579 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 0.36 (10579 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31439866T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288587	ENST00000673857.1	n.63-23257T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55012 AN: 151354 Hom.: 10566 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.364 AC: 55077 AN: 151470 Hom.: 10579 Cov.: 31 AF XY: 0.367 AC XY: 27191 AN XY: 74012

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.387

Alfa AF: 0.311 Hom.: 12726

Bravo AF: 0.371

Asia WGS AF: 0.378 AC: 1311 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7772549; hg19: chr6-31407643;