rs4831837

Variant names:

• chr8-12854354-G-A
• rs4831837
• ENST00000838107.1:n.328+9513C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-12854354-G-A
• chr8-12854354-G-C

Variant summary

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

The ENST00000838107.1(ENSG00000309058):​n.328+9513C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,946 control chromosomes in the GnomAD database, including 21,575 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 (21575 hom., cov: 32)
• Consequence: ENSG00000309058 ENST00000838107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 11 publications found

Genes affected

ENSG00000309058 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.605 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
ENSG00000309058	ENST00000838107.1	n.328+9513C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79965 AN: 151826 Hom.: 21564 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.527 AC: 80002 AN: 151946 Hom.: 21575 Cov.: 32 AF XY: 0.524 AC XY: 38928 AN XY: 74260

African (AFR) AF: 0.422 AC: 17489 AN: 41418

American (AMR) AF: 0.615 AC: 9403 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1896 AN: 3472

East Asian (EAS) AF: 0.607 AC: 3137 AN: 5164

South Asian (SAS) AF: 0.394 AC: 1903 AN: 4824

European-Finnish (FIN) AF: 0.557 AC: 5859 AN: 10528

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38414 AN: 67954

Other (OTH) AF: 0.566 AC: 1189 AN: 2102

Alfa AF: 0.558 Hom.: 101743

Bravo AF: 0.531

Asia WGS AF: 0.525 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.67
DANN	Benign	0.53
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs4831837; hg19: chr8-12711863;