chr10-59628610-G-A

Variant names:

• chr10-59628610-G-A
• rs16913885
• ENST00000644636.1:n.371G>A

Variant summary

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

The ENST00000644636.1(ENSG00000235140):​n.371G>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 0.158 in 152,192 control chromosomes in the GnomAD database, including 2,059 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 0.16 (2058 hom., cov: 32)
  • Exomes 𝑓: 0.068 (1 hom.)
• Consequence: ENSG00000235140 ENST00000644636.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

Genes affected

ENSG00000235140 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.205 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
ENSG00000235140	ENST00000644636.1	n.371G>A		non_coding_transcript_exon_variant	Exon 4 of 7

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24079 AN: 152030 Hom.: 2059 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0827

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.164

GnomAD4 exome AF: 0.0682 AC: 3 AN: 44 Hom.: 1 Cov.: 0 AF XY: 0.0294 AC XY: 1 AN XY: 34

Gnomad4 NFE exome AF: 0.0500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.158 AC: 24080 AN: 152148 Hom.: 2058 Cov.: 32 AF XY: 0.159 AC XY: 11853 AN XY: 74380

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.0823

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.163

Alfa AF: 0.138 Hom.: 3138

Bravo AF: 0.162

Asia WGS AF: 0.134 AC: 470 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	5.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16913885; hg19: chr10-61388368;