chr10-47139553-G-A

Variant names:

• chr10-47139553-G-A
• rs6588761
• ENST00000740894.1:n.1256G>A

Variant summary

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

The ENST00000740894.1(ENSG00000296622):​n.1256G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0848 in 151,968 control chromosomes in the GnomAD database, including 1,255 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 0.085 (1255 hom., cov: 30)
• Consequence: ENSG00000296622 ENST00000740894.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990
• Publications: 1 publications found

Genes affected

ENSG00000296622 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740894.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296622	ENST00000740894.1		n.1256G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000296622	ENST00000740895.1		n.391G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000296622	ENST00000740878.1		n.380+1397G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12850 AN: 151850 Hom.: 1251 Cov.: 30

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.00547

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0844

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

GnomAD4 genome AF: 0.0848 AC: 12880 AN: 151968 Hom.: 1255 Cov.: 30 AF XY: 0.0814 AC XY: 6049 AN XY: 74298

African (AFR) AF: 0.239 AC: 9869 AN: 41324

American (AMR) AF: 0.0540 AC: 826 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 341 AN: 3462

East Asian (EAS) AF: 0.000968 AC: 5 AN: 5164

South Asian (SAS) AF: 0.0123 AC: 59 AN: 4812

European-Finnish (FIN) AF: 0.00547 AC: 58 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0222 AC: 1507 AN: 68002

Other (OTH) AF: 0.0835 AC: 176 AN: 2108

Alfa AF: 0.0661 Hom.: 117

Bravo AF: 0.0965

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.83
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs6588761; hg19: chr10-48599809;