rs10514718

Variant names:

• chr3-61428140-C-G
• rs10514718
• ENST00000836317.1:n.142+374G>C

Your query was ambiguous. Multiple possible variants found:

• chr3-61428140-C-G
• chr3-61428140-C-T

Variant summary

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

The ENST00000836317.1(ENSG00000308777):​n.142+374G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 152,114 control chromosomes in the GnomAD database, including 425 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 0.067 (425 hom., cov: 31)
• Consequence: ENSG00000308777 ENST00000836317.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 13 publications found

Genes affected

ENSG00000308777 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836317.1. 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
	ENSG00000308777	ENST00000836317.1		n.142+374G>C		intron	N/A
	ENSG00000308777	ENST00000836318.1		n.128+374G>C		intron	N/A
	ENSG00000308777	ENST00000836319.1		n.128+374G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10142 AN: 151996 Hom.: 424 Cov.: 31

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0684

Gnomad ASJ AF: 0.0554

Gnomad EAS AF: 0.0599

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0668 AC: 10165 AN: 152114 Hom.: 425 Cov.: 31 AF XY: 0.0706 AC XY: 5248 AN XY: 74350

African (AFR) AF: 0.0850 AC: 3526 AN: 41476

American (AMR) AF: 0.0686 AC: 1047 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0554 AC: 192 AN: 3466

East Asian (EAS) AF: 0.0602 AC: 311 AN: 5166

South Asian (SAS) AF: 0.141 AC: 679 AN: 4816

European-Finnish (FIN) AF: 0.0912 AC: 964 AN: 10574

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0482 AC: 3277 AN: 68028

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0520 Hom.: 147

Bravo AF: 0.0646

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	16
DANN	Benign	0.67
PhyloP100		0.40

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: rs10514718;

hg19: chr3-61413814;