rs311390

Variant names:

• chr8-54189841-G-A
• rs311390
• ENST00000728273.1:n.48-1742G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-54189841-G-A
• chr8-54189841-G-C
• chr8-54189841-G-T

Variant summary

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

The ENST00000728273.1(ENSG00000295151):​n.48-1742G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,964 control chromosomes in the GnomAD database, including 29,979 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 0.63 (29979 hom., cov: 32)
• Consequence: ENSG00000295151 ENST00000728273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 0 publications found

Genes affected

ENSG00000295151 (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 (NFE) allele frequency at 95% confidence interval = 0.643 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
ENSG00000295151	ENST00000728273.1	n.48-1742G>A		intron_variant	Intron 1 of 2
ENSG00000295151	ENST00000728274.1	n.87-18012G>A		intron_variant	Intron 1 of 1
ENSG00000295151	ENST00000728275.1	n.86-1742G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94949 AN: 151848 Hom.: 29972 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.625 AC: 95008 AN: 151964 Hom.: 29979 Cov.: 32 AF XY: 0.623 AC XY: 46270 AN XY: 74288

African (AFR) AF: 0.630 AC: 26118 AN: 41440

American (AMR) AF: 0.516 AC: 7880 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2195 AN: 3470

East Asian (EAS) AF: 0.582 AC: 3005 AN: 5162

South Asian (SAS) AF: 0.522 AC: 2522 AN: 4828

European-Finnish (FIN) AF: 0.669 AC: 7055 AN: 10540

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

European-Non Finnish (NFE) AF: 0.648 AC: 44051 AN: 67950

Other (OTH) AF: 0.634 AC: 1336 AN: 2106

Alfa AF: 0.639 Hom.: 18148

Bravo AF: 0.617

Asia WGS AF: 0.525 AC: 1829 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	2.5
DANN	Benign	0.52
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs311390; hg19: chr8-55102401;