rs4456181

Variant names:

• chr10-71020923-G-A
• rs4456181
• ENST00000646051.1:n.259-5656G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-71020923-G-A
• chr10-71020923-G-C
• chr10-71020923-G-T

Variant summary

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

The ENST00000646051.1(ENSG00000285300):​n.259-5656G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,160 control chromosomes in the GnomAD database, including 42,812 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 0.75 (42812 hom., cov: 32)
• Consequence: ENSG00000285300 ENST00000646051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 0 publications found

Genes affected

ENSG00000285300 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646051.1. 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
	ENSG00000285300	ENST00000646051.1		n.259-5656G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113704 AN: 152042 Hom.: 42776 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.748 AC: 113786 AN: 152160 Hom.: 42812 Cov.: 32 AF XY: 0.746 AC XY: 55540 AN XY: 74404

African (AFR) AF: 0.697 AC: 28938 AN: 41504

American (AMR) AF: 0.679 AC: 10371 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2854 AN: 3472

East Asian (EAS) AF: 0.735 AC: 3809 AN: 5180

South Asian (SAS) AF: 0.657 AC: 3168 AN: 4822

European-Finnish (FIN) AF: 0.819 AC: 8676 AN: 10592

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53416 AN: 67994

Other (OTH) AF: 0.759 AC: 1603 AN: 2112

Alfa AF: 0.755 Hom.: 7820

Bravo AF: 0.737

Asia WGS AF: 0.699 AC: 2430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.62
PhyloP100		-1.7

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: rs4456181;

hg19: chr10-72780680;