rs150724

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000261743 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561595.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261743	ENST00000561595.1	TSL:4	n.195A>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000260658	ENST00000568932.5	TSL:5	n.435-34371T>G		intron	N/A
	ENSG00000260658	ENST00000734799.1		n.435-34371T>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.814 AC: 33681 AN: 41402

American (AMR) AF: 0.695 AC: 10599 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3470

East Asian (EAS) AF: 0.878 AC: 4518 AN: 5144

South Asian (SAS) AF: 0.636 AC: 3053 AN: 4800

European-Finnish (FIN) AF: 0.635 AC: 6690 AN: 10538

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46272 AN: 67930

Other (OTH) AF: 0.742 AC: 1562 AN: 2104

Alfa AF: 0.691 Hom.: 21390

Bravo AF: 0.732

Asia WGS AF: 0.768 AC: 2670 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.79
PhyloP100		-0.61

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs150724;

hg19: chr16-63402942;