13-71872548-A-G

Variant names:

• chr13-71872548-A-G
• rs3818437
• ENST00000719679.1:n.318+4787A>G

Variant summary

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

The ENST00000719679.1(ENSG00000293895):​n.318+4787A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,034 control chromosomes in the GnomAD database, including 56,347 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 0.83 (56347 hom., cov: 32)
• Consequence: ENSG00000293895 ENST00000719679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 0 publications found

Genes affected

ENSG00000293895 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 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
ENSG00000293895	ENST00000719679.1	n.318+4787A>G		intron_variant	Intron 1 of 1
ENSG00000293895	ENST00000719680.1	n.117-3456A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126576 AN: 151916 Hom.: 56342 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.833 AC: 126620 AN: 152034 Hom.: 56347 Cov.: 32 AF XY: 0.834 AC XY: 61971 AN XY: 74314

African (AFR) AF: 0.520 AC: 21517 AN: 41404

American (AMR) AF: 0.879 AC: 13427 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3423 AN: 3472

East Asian (EAS) AF: 0.508 AC: 2619 AN: 5156

South Asian (SAS) AF: 0.939 AC: 4518 AN: 4812

European-Finnish (FIN) AF: 0.980 AC: 10402 AN: 10616

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67690 AN: 67984

Other (OTH) AF: 0.865 AC: 1827 AN: 2112

Alfa AF: 0.882 Hom.: 7121

Bravo AF: 0.809

Asia WGS AF: 0.754 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.65
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs3818437; hg19: chr13-72446686;