rs16913885

Positions:

• chr10-59628610-G-A
• chr10-59628610-G-C

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: ENST00000644636.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644636.1	n.371G>A		non_coding_transcript_exon_variant	4/7

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;