6-31439866-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 31 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673857.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288587	ENST00000673857.1		n.63-23257T>C		intron	N/A

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

African (AFR) AF: 0.448 AC: 18435 AN: 41120

American (AMR) AF: 0.418 AC: 6330 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1650 AN: 5138

South Asian (SAS) AF: 0.325 AC: 1560 AN: 4806

European-Finnish (FIN) AF: 0.371 AC: 3910 AN: 10538

Middle Eastern (MID) AF: 0.455 AC: 131 AN: 288

European-Non Finnish (NFE) AF: 0.296 AC: 20135 AN: 67950

Other (OTH) AF: 0.387 AC: 815 AN: 2106

Alfa AF: 0.319 Hom.: 22155

Bravo AF: 0.371

Asia WGS AF: 0.378 AC: 1311 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7772549;

hg19: chr6-31407643;