6-31352761-C-T

Variant names:

• chr6-31352761-C-T
• rs2442719
• ENST00000755297.1:n.33-3440C>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-3440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,878 control chromosomes in the GnomAD database, including 21,722 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 0.53 (21722 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 51 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.581 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
ENSG00000298396	ENST00000755297.1	n.33-3440C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80361 AN: 151758 Hom.: 21710 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.530 AC: 80432 AN: 151878 Hom.: 21722 Cov.: 31 AF XY: 0.528 AC XY: 39202 AN XY: 74212

African (AFR) AF: 0.487 AC: 20136 AN: 41386

American (AMR) AF: 0.554 AC: 8465 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2065 AN: 3468

East Asian (EAS) AF: 0.326 AC: 1683 AN: 5162

South Asian (SAS) AF: 0.599 AC: 2884 AN: 4812

European-Finnish (FIN) AF: 0.473 AC: 4984 AN: 10536

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38245 AN: 67944

Other (OTH) AF: 0.558 AC: 1169 AN: 2096

Alfa AF: 0.552 Hom.: 87451

Bravo AF: 0.534

Asia WGS AF: 0.521 AC: 1813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.8
DANN	Benign	0.75
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2442719; hg19: chr6-31320538;