chr6-31439866-T-C

Variant names:

• chr6-31439866-T-C
• rs7772549
• ENST00000673857.1:n.63-23257T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000673857.1(ENSG00000288587):​n.63-23257T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

Genes affected

ENSG00000288587 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288587	ENST00000673857.1	n.63-23257T>C		intron_variant	Intron 1 of 2

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;