6-31279637-C-T

Variant names:

• chr6-31279637-C-T
• rs2844608
• ENST00000755297.1:n.32+8531C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000755297.1(ENSG00000298396):​n.32+8531C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,900 control chromosomes in the GnomAD database, including 11,888 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 0.39 (11888 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 6 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. 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
	ENSG00000298396	ENST00000755297.1		n.32+8531C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59684 AN: 151782 Hom.: 11873 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.393 AC: 59731 AN: 151900 Hom.: 11888 Cov.: 32 AF XY: 0.395 AC XY: 29293 AN XY: 74222

African (AFR) AF: 0.401 AC: 16633 AN: 41438

American (AMR) AF: 0.442 AC: 6758 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1456 AN: 3468

East Asian (EAS) AF: 0.431 AC: 2220 AN: 5154

South Asian (SAS) AF: 0.342 AC: 1643 AN: 4810

European-Finnish (FIN) AF: 0.441 AC: 4628 AN: 10506

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25144 AN: 67928

Other (OTH) AF: 0.388 AC: 820 AN: 2112

Alfa AF: 0.357 Hom.: 1199

Bravo AF: 0.392

Asia WGS AF: 0.383 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.19
PhyloP100		0.052

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: rs2844608;

hg19: chr6-31247414;