rs1876511

Variant names:

• chr8-10021773-A-C
• rs1876511
• ENST00000659604.1:n.117-31076T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-10021773-A-C
• chr8-10021773-A-T

Variant summary

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

The ENST00000659604.1(MSRA-DT):​n.117-31076T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,214 control chromosomes in the GnomAD database, including 2,222 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 0.15 (2222 hom., cov: 33)
• Consequence: MSRA-DT ENST00000659604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSRA-DT	ENST00000659604.1	n.117-31076T>G		intron_variant	Intron 1 of 2
MSRA-DT	ENST00000843173.1	n.33-31076T>G		intron_variant	Intron 1 of 3
MSRA-DT	ENST00000843174.1	n.233+29987T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22111 AN: 152096 Hom.: 2226 Cov.: 33

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.145 AC: 22103 AN: 152214 Hom.: 2222 Cov.: 33 AF XY: 0.155 AC XY: 11560 AN XY: 74418

African (AFR) AF: 0.0456 AC: 1894 AN: 41564

American (AMR) AF: 0.215 AC: 3279 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3470

East Asian (EAS) AF: 0.443 AC: 2289 AN: 5166

South Asian (SAS) AF: 0.286 AC: 1377 AN: 4818

European-Finnish (FIN) AF: 0.244 AC: 2582 AN: 10578

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9624 AN: 68016

Other (OTH) AF: 0.151 AC: 319 AN: 2110

Alfa AF: 0.130 Hom.: 627

Bravo AF: 0.143

Asia WGS AF: 0.320 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.57
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1876511; hg19: chr8-9879283;