rs132617

Variant names:

• chr22-36137737-C-T
• rs132617
• ENST00000624395.1:n.1614G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000624395.1(ENSG00000279805):​n.1614G>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 0.321 in 152,042 control chromosomes in the GnomAD database, including 8,046 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 0.32 (8045 hom., cov: 32)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: ENSG00000279805 ENST00000624395.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 7 publications found

Genes affected

ENSG00000279805 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624395.1. 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
	ENSG00000279805	ENST00000624395.1	TSL:6	n.1614G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48748 AN: 151916 Hom.: 8035 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.321 AC: 48794 AN: 152034 Hom.: 8045 Cov.: 32 AF XY: 0.323 AC XY: 24038 AN XY: 74318

African (AFR) AF: 0.253 AC: 10491 AN: 41446

American (AMR) AF: 0.292 AC: 4455 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3468

East Asian (EAS) AF: 0.214 AC: 1109 AN: 5174

South Asian (SAS) AF: 0.405 AC: 1948 AN: 4810

European-Finnish (FIN) AF: 0.413 AC: 4362 AN: 10562

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24186 AN: 67980

Other (OTH) AF: 0.295 AC: 624 AN: 2112

Alfa AF: 0.341 Hom.: 27068

Bravo AF: 0.306

Asia WGS AF: 0.349 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		0.096

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: rs132617;

hg19: chr22-36533785;