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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267902	XR_926691.3	n.964+810A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298396	ENST00000755297.1	n.32+34862T>C		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs3873386; hg19: chr6-31273745;