rs4996815

Variant names:

• chr13-105999312-G-T
• rs4996815
• ENST00000657278.1:n.1796-46317C>A

Variant summary

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

The ENST00000657278.1(ENSG00000287923):​n.1796-46317C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 151,952 control chromosomes in the GnomAD database, including 28,628 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 0.60 (28628 hom., cov: 31)
• Consequence: ENSG00000287923 ENST00000657278.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 7 publications found

Genes affected

ENSG00000287923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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
ENSG00000287923	ENST00000657278.1	n.1796-46317C>A		intron_variant	Intron 1 of 2
ENSG00000287923	ENST00000670458.1	n.1563-46317C>A		intron_variant	Intron 1 of 2
ENSG00000287923	ENST00000754737.1	n.416-46317C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91316 AN: 151834 Hom.: 28614 Cov.: 31

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.601 AC: 91360 AN: 151952 Hom.: 28628 Cov.: 31 AF XY: 0.589 AC XY: 43722 AN XY: 74276

African (AFR) AF: 0.664 AC: 27509 AN: 41436

American (AMR) AF: 0.478 AC: 7298 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1950 AN: 3470

East Asian (EAS) AF: 0.0744 AC: 383 AN: 5150

South Asian (SAS) AF: 0.528 AC: 2538 AN: 4808

European-Finnish (FIN) AF: 0.538 AC: 5676 AN: 10542

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43996 AN: 67962

Other (OTH) AF: 0.549 AC: 1159 AN: 2110

Alfa AF: 0.619 Hom.: 122118

Bravo AF: 0.594

Asia WGS AF: 0.313 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.54
DANN	Benign	0.68
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4996815; hg19: chr13-106651661;