6-31305968-T-C

Variant names:

• chr6-31305968-T-C
• rs3873386
• ENST00000755297.1:n.32+34862T>C

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+34862T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,932 control chromosomes in the GnomAD database, including 15,675 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 0.45 (15675 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94
• Publications: 42 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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+34862T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67998 AN: 151814 Hom.: 15649 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.448 AC: 68064 AN: 151932 Hom.: 15675 Cov.: 31 AF XY: 0.455 AC XY: 33756 AN XY: 74268

African (AFR) AF: 0.532 AC: 22041 AN: 41402

American (AMR) AF: 0.488 AC: 7457 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1285 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1723 AN: 5170

South Asian (SAS) AF: 0.500 AC: 2411 AN: 4820

European-Finnish (FIN) AF: 0.523 AC: 5508 AN: 10538

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26278 AN: 67936

Other (OTH) AF: 0.447 AC: 943 AN: 2108

Alfa AF: 0.407 Hom.: 52983

Bravo AF: 0.449

Asia WGS AF: 0.422 AC: 1468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.50
PhyloP100		-2.9

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: rs3873386;

hg19: chr6-31273745;