10-111583938-A-G

Variant names:

• chr10-111583938-A-G
• rs1855962
• ENST00000829409.1:n.116+51121T>C

Variant summary

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

The ENST00000829409.1(ENSG00000307856):​n.116+51121T>C variant causes a intron change. The variant allele was found at a frequency of 0.0779 in 152,336 control chromosomes in the GnomAD database, including 723 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 0.078 (723 hom., cov: 34)
• Consequence: ENSG00000307856 ENST00000829409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 1 publications found

Genes affected

ENSG00000307856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829409.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307856	ENST00000829409.1		n.116+51121T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11847 AN: 152218 Hom.: 717 Cov.: 34

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0714

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0779 AC: 11867 AN: 152336 Hom.: 723 Cov.: 34 AF XY: 0.0800 AC XY: 5960 AN XY: 74488

African (AFR) AF: 0.157 AC: 6517 AN: 41568

American (AMR) AF: 0.0395 AC: 605 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.0714 AC: 248 AN: 3472

East Asian (EAS) AF: 0.146 AC: 755 AN: 5176

South Asian (SAS) AF: 0.175 AC: 843 AN: 4826

European-Finnish (FIN) AF: 0.0378 AC: 402 AN: 10628

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0342 AC: 2327 AN: 68032

Other (OTH) AF: 0.0704 AC: 149 AN: 2116

Alfa AF: 0.0602 Hom.: 60

Bravo AF: 0.0780

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.6
DANN	Benign	0.32

Splicing

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

Other links and lift over

dbSNP: rs1855962; hg19: chr10-113343696;