rs1816678

Variant names:

• chr5-111060457-A-G
• rs1816678
• ENST00000743602.1:n.29+5978T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-111060457-A-G
• chr5-111060457-A-T

Variant summary

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

The ENST00000743602.1(ENSG00000296915):​n.29+5978T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,138 control chromosomes in the GnomAD database, including 30,687 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 0.62 (30687 hom., cov: 33)
• Consequence: ENSG00000296915 ENST00000743602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.13
• Publications: 2 publications found

Genes affected

ENSG00000296915 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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
ENSG00000296915	ENST00000743602.1	n.29+5978T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94102 AN: 152020 Hom.: 30652 Cov.: 33

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.619 AC: 94186 AN: 152138 Hom.: 30687 Cov.: 33 AF XY: 0.618 AC XY: 45937 AN XY: 74372

African (AFR) AF: 0.837 AC: 34740 AN: 41528

American (AMR) AF: 0.624 AC: 9542 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3468

East Asian (EAS) AF: 0.602 AC: 3116 AN: 5174

South Asian (SAS) AF: 0.531 AC: 2561 AN: 4822

European-Finnish (FIN) AF: 0.479 AC: 5060 AN: 10556

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35114 AN: 67974

Other (OTH) AF: 0.610 AC: 1290 AN: 2114

Alfa AF: 0.567 Hom.: 3150

Bravo AF: 0.644

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0030
DANN	Benign	0.29
PhyloP100		-6.1

Splicing

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

Other links and lift over

dbSNP: rs1816678; hg19: chr5-110396155;