8-10021941-C-G

Variant names:

• chr8-10021941-C-G
• rs613080
• ENST00000659604.1:n.117-31244G>C

Variant summary

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

The ENST00000659604.1(MSRA-DT):​n.117-31244G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 151,986 control chromosomes in the GnomAD database, including 56,492 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 0.86 (56492 hom., cov: 29)
• Consequence: MSRA-DT ENST00000659604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• Publications: 4 publications found

Genes affected

MSRA-DT (HGNC:55400): (MSRA divergent transcript)

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 (AFR) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659604.1. 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
	MSRA-DT	ENST00000659604.1		n.117-31244G>C		intron	N/A
	MSRA-DT	ENST00000843173.1		n.33-31244G>C		intron	N/A
	MSRA-DT	ENST00000843174.1		n.233+29819G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130170 AN: 151868 Hom.: 56430 Cov.: 29

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.857 AC: 130295 AN: 151986 Hom.: 56492 Cov.: 29 AF XY: 0.847 AC XY: 62903 AN XY: 74270

African (AFR) AF: 0.957 AC: 39726 AN: 41494

American (AMR) AF: 0.786 AC: 12000 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3070 AN: 3470

East Asian (EAS) AF: 0.558 AC: 2868 AN: 5136

South Asian (SAS) AF: 0.714 AC: 3419 AN: 4790

European-Finnish (FIN) AF: 0.762 AC: 8016 AN: 10524

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58468 AN: 67992

Other (OTH) AF: 0.853 AC: 1806 AN: 2116

Alfa AF: 0.834 Hom.: 2640

Bravo AF: 0.860

Asia WGS AF: 0.689 AC: 2400 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	0.10
DANN	Benign	0.40
PhyloP100		-0.99

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: rs613080;

hg19: chr8-9879451;