rs10516343

Variant names:

• chr4-19973239-C-A
• rs10516343
• ENST00000819373.1:n.111+35689C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-19973239-C-A
• chr4-19973239-C-G

Variant summary

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

The ENST00000819373.1(ENSG00000248515):​n.111+35689C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,198 control chromosomes in the GnomAD database, including 49,168 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 0.80 (49168 hom., cov: 32)
• Consequence: ENSG00000248515 ENST00000819373.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 3 publications found

Genes affected

ENSG00000248515 (HGNC:59079):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819373.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248515	ENST00000819373.1		n.111+35689C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121915 AN: 152080 Hom.: 49118 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.802 AC: 122023 AN: 152198 Hom.: 49168 Cov.: 32 AF XY: 0.803 AC XY: 59718 AN XY: 74394

African (AFR) AF: 0.886 AC: 36816 AN: 41536

American (AMR) AF: 0.789 AC: 12058 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2878 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4210 AN: 5170

South Asian (SAS) AF: 0.787 AC: 3805 AN: 4832

European-Finnish (FIN) AF: 0.747 AC: 7910 AN: 10588

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51841 AN: 68004

Other (OTH) AF: 0.815 AC: 1723 AN: 2114

Alfa AF: 0.778 Hom.: 180497

Bravo AF: 0.807

Asia WGS AF: 0.790 AC: 2748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.055
DANN	Benign	0.22
PhyloP100		-2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10516343;

hg19: chr4-19974862;