rs10455776

Variant names:

• chr6-159578848-G-T
• rs10455776
• ENST00000656085.1:n.42+83738C>A

Variant summary

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

The ENST00000656085.1(ENSG00000286533):​n.42+83738C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,168 control chromosomes in the GnomAD database, including 2,122 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 0.16 (2122 hom., cov: 32)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 5 publications found

Genes affected

ENSG00000286533 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656085.1. 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
	ENSG00000286533	ENST00000656085.1		n.42+83738C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24135 AN: 152052 Hom.: 2117 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0673

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.159 AC: 24159 AN: 152168 Hom.: 2122 Cov.: 32 AF XY: 0.159 AC XY: 11818 AN XY: 74384

African (AFR) AF: 0.242 AC: 10043 AN: 41482

American (AMR) AF: 0.127 AC: 1936 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3468

East Asian (EAS) AF: 0.0675 AC: 349 AN: 5174

South Asian (SAS) AF: 0.179 AC: 863 AN: 4820

European-Finnish (FIN) AF: 0.143 AC: 1510 AN: 10594

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8746 AN: 68022

Other (OTH) AF: 0.138 AC: 292 AN: 2112

Alfa AF: 0.145 Hom.: 317

Bravo AF: 0.157

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.38
DANN	Benign	0.41
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10455776; hg19: chr6-159999880;