rs1739646

Variant names:

• chr20-38408937-T-C
• rs1739646
• ENST00000422519.2:n.1693-2615A>G

Variant summary

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

The ENST00000422519.2(ENSG00000224635):​n.1693-2615A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,086 control chromosomes in the GnomAD database, including 4,152 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 0.22 (4152 hom., cov: 32)
• Consequence: ENSG00000224635 ENST00000422519.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.720
• Publications: 10 publications found

Genes affected

ENSG00000224635 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422519.2. 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
	ENSG00000224635	ENST00000422519.2	TSL:2	n.1693-2615A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32866 AN: 151968 Hom.: 4139 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.210

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.216 AC: 32919 AN: 152086 Hom.: 4152 Cov.: 32 AF XY: 0.214 AC XY: 15898 AN XY: 74334

African (AFR) AF: 0.350 AC: 14518 AN: 41440

American (AMR) AF: 0.170 AC: 2595 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 668 AN: 3470

East Asian (EAS) AF: 0.0929 AC: 481 AN: 5176

South Asian (SAS) AF: 0.202 AC: 976 AN: 4826

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10582

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11647 AN: 68004

Other (OTH) AF: 0.209 AC: 442 AN: 2112

Alfa AF: 0.183 Hom.: 2010

Bravo AF: 0.224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
PhyloP100		0.72

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: rs1739646;

hg19: chr20-37037584;