chr8-10002570-G-C

Variant names:

• chr8-10002570-G-C
• rs545854
• ENST00000659604.1:n.117-11873C>G

Variant summary

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

The ENST00000659604.1(MSRA-DT):​n.117-11873C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,132 control chromosomes in the GnomAD database, including 55,139 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 0.85 (55139 hom., cov: 30)
• Consequence: MSRA-DT ENST00000659604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654
• Publications: 46 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 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.117-11873C>G		intron	N/A
	MSRA-DT	ENST00000843173.1		n.33-11873C>G		intron	N/A
	MSRA-DT	ENST00000843174.1		n.234-11873C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128667 AN: 152014 Hom.: 55077 Cov.: 30

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.847 AC: 128788 AN: 152132 Hom.: 55139 Cov.: 30 AF XY: 0.839 AC XY: 62368 AN XY: 74344

African (AFR) AF: 0.955 AC: 39640 AN: 41510

American (AMR) AF: 0.779 AC: 11910 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3049 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2985 AN: 5146

South Asian (SAS) AF: 0.652 AC: 3134 AN: 4806

European-Finnish (FIN) AF: 0.797 AC: 8430 AN: 10582

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56957 AN: 68008

Other (OTH) AF: 0.840 AC: 1771 AN: 2108

Alfa AF: 0.856 Hom.: 7027

Bravo AF: 0.847

Asia WGS AF: 0.671 AC: 2339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs545854; hg19: chr8-9860080;