rs10875595

Positions:

• chr5-141320922-T-G

Variant summary

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

The ENST00000701867.1(ENSG00000288095):​n.13T>G 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 0.142 in 157,418 control chromosomes in the GnomAD database, including 1,745 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 0.14 (1672 hom., cov: 33)
  • Exomes 𝑓: 0.17 (73 hom.)
• Consequence: ENST00000701867.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 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
	ENST00000701867.1	n.13T>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21543 AN: 152230 Hom.: 1671 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.132

GnomAD4 exome AF: 0.168 AC: 850 AN: 5070 Hom.: 73 AF XY: 0.172 AC XY: 437 AN XY: 2544

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.235

Gnomad4 OTH exome AF: 0.192

GnomAD4 genome AF: 0.141 AC: 21548 AN: 152348 Hom.: 1672 Cov.: 33 AF XY: 0.140 AC XY: 10419 AN XY: 74500

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0670

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.132

Alfa AF: 0.159 Hom.: 2509

Bravo AF: 0.133

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10875595; hg19: chr5-140700489;