10-87555668-G-T

Variant names:

• chr10-87555668-G-T
• rs2077871
• ENST00000804693.1:n.212-1736C>A

Variant summary

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

The ENST00000804693.1(ENSG00000223761):​n.212-1736C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,590 control chromosomes in the GnomAD database, including 27,815 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 0.60 (27815 hom., cov: 30)
• Consequence: ENSG00000223761 ENST00000804693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.477
• Publications: 3 publications found

Genes affected

ENSG00000223761 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804693.1. 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
	ENSG00000223761	ENST00000804693.1		n.212-1736C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91285 AN: 151472 Hom.: 27782 Cov.: 30

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.603 AC: 91372 AN: 151590 Hom.: 27815 Cov.: 30 AF XY: 0.603 AC XY: 44636 AN XY: 74034

African (AFR) AF: 0.698 AC: 28886 AN: 41390

American (AMR) AF: 0.614 AC: 9363 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1712 AN: 3464

East Asian (EAS) AF: 0.687 AC: 3541 AN: 5152

South Asian (SAS) AF: 0.510 AC: 2447 AN: 4798

European-Finnish (FIN) AF: 0.573 AC: 6011 AN: 10498

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37554 AN: 67734

Other (OTH) AF: 0.582 AC: 1226 AN: 2106

Alfa AF: 0.558 Hom.: 25586

Bravo AF: 0.613

Asia WGS AF: 0.597 AC: 2072 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.4
DANN	Benign	0.65
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs2077871; hg19: chr10-89315425;