rs7081156

Variant names:

• chr10-20553102-T-C
• rs7081156
• ENST00000785943.1:n.367+37332T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-20553102-T-C
• chr10-20553102-T-G

Variant summary

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

The ENST00000785943.1(ENSG00000302338):​n.367+37332T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 150,708 control chromosomes in the GnomAD database, including 2,086 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 0.13 (2086 hom., cov: 29)
• Consequence: ENSG00000302338 ENST00000785943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 5 publications found

Genes affected

ENSG00000302338 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785943.1. 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
	ENSG00000302338	ENST00000785943.1		n.367+37332T>C		intron	N/A
	ENSG00000302338	ENST00000785944.1		n.280+37332T>C		intron	N/A
	ENSG00000302338	ENST00000785945.1		n.214+37332T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18865 AN: 150596 Hom.: 2081 Cov.: 29

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.125 AC: 18895 AN: 150708 Hom.: 2086 Cov.: 29 AF XY: 0.121 AC XY: 8934 AN XY: 73616

African (AFR) AF: 0.288 AC: 11718 AN: 40724

American (AMR) AF: 0.0765 AC: 1157 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 701 AN: 3460

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5152

South Asian (SAS) AF: 0.118 AC: 559 AN: 4754

European-Finnish (FIN) AF: 0.0267 AC: 277 AN: 10376

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.0609 AC: 4128 AN: 67836

Other (OTH) AF: 0.121 AC: 253 AN: 2084

Alfa AF: 0.0941 Hom.: 2383

Bravo AF: 0.141

Asia WGS AF: 0.0670 AC: 234 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		0.057

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: rs7081156;

hg19: chr10-20842031;