chr8-10054107-C-T

Position:

• chr8-10054107-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000562143.1(MSRA-DT):​n.148G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 156,812 control chromosomes in the GnomAD database, including 35,440 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 0.65 (34115 hom., cov: 33)
  • Exomes 𝑓: 0.75 (1325 hom.)
• Consequence: MSRA-DT ENST00000562143.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSRA-DT	ENST00000562143.1	n.148G>A		non_coding_transcript_exon_variant	1/1
	ENST00000659604.1	n.116+819G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99529 AN: 152054 Hom.: 34135 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.701

GnomAD4 exome AF: 0.751 AC: 3485 AN: 4640 Hom.: 1325 Cov.: 0 AF XY: 0.754 AC XY: 1658 AN XY: 2198

Gnomad4 AFR exome AF: 0.408

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.820

Gnomad4 EAS exome AF: 0.546

Gnomad4 SAS exome AF: 0.791

Gnomad4 FIN exome AF: 0.816

Gnomad4 NFE exome AF: 0.771

Gnomad4 OTH exome AF: 0.727

GnomAD4 genome AF: 0.654 AC: 99517 AN: 152172 Hom.: 34115 Cov.: 33 AF XY: 0.655 AC XY: 48710 AN XY: 74388

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.692

Alfa AF: 0.736 Hom.: 41113

Bravo AF: 0.632

Asia WGS AF: 0.620 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.3
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10098474; hg19: chr8-9911617;