rs2185710

Variant names:

• chr6-113055846-A-G
• rs2185710
• ENST00000670062.1:n.479+5333A>G

Variant summary

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

The ENST00000670062.1(ENSG00000288560):​n.479+5333A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,830 control chromosomes in the GnomAD database, including 21,353 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 0.51 (21353 hom., cov: 30)
• Consequence: ENSG00000288560 ENST00000670062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 3 publications found

Genes affected

ENSG00000288560 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670062.1. 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
	ENSG00000288560	ENST00000670062.1		n.479+5333A>G		intron	N/A
	ENSG00000288560	ENST00000737247.1		n.237+5333A>G		intron	N/A
	ENSG00000288560	ENST00000737248.1		n.73+5333A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77889 AN: 151712 Hom.: 21352 Cov.: 30

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.513 AC: 77916 AN: 151830 Hom.: 21353 Cov.: 30 AF XY: 0.514 AC XY: 38158 AN XY: 74210

African (AFR) AF: 0.305 AC: 12642 AN: 41432

American (AMR) AF: 0.554 AC: 8435 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1830 AN: 3464

East Asian (EAS) AF: 0.454 AC: 2342 AN: 5158

South Asian (SAS) AF: 0.562 AC: 2714 AN: 4826

European-Finnish (FIN) AF: 0.618 AC: 6516 AN: 10548

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41544 AN: 67866

Other (OTH) AF: 0.516 AC: 1086 AN: 2106

Alfa AF: 0.564 Hom.: 36383

Bravo AF: 0.498

Asia WGS AF: 0.527 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		0.39

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: rs2185710;

hg19: chr6-113377048;