rs150724

Variant names:

• chr16-63369038-A-C
• rs150724
• ENST00000561595.1:n.195A>C

Variant summary

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

The ENST00000561595.1(ENSG00000261743):​n.195A>C 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 0.722 in 151,846 control chromosomes in the GnomAD database, including 39,924 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 0.72 (39924 hom., cov: 30)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000261743 ENST00000561595.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608

Genes affected

ENSG00000261743 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371308	XR_001752232.2	n.435-34371T>G		intron_variant	Intron 2 of 5
LOC105371308	XR_007065220.1	n.435-34371T>G		intron_variant	Intron 2 of 3
LOC105371308	XR_007065221.1	n.435-34371T>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261743	ENST00000561595.1	n.195A>C		non_coding_transcript_exon_variant	Exon 1 of 2	4
ENSG00000260658	ENST00000568932.5	n.435-34371T>G		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109561 AN: 151726 Hom.: 39878 Cov.: 30

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.739

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.722 AC: 109661 AN: 151844 Hom.: 39924 Cov.: 30 AF XY: 0.718 AC XY: 53319 AN XY: 74226

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.742

Alfa AF: 0.690 Hom.: 19270

Bravo AF: 0.732

Asia WGS AF: 0.768 AC: 2670 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs150724; hg19: chr16-63402942;