rs1739646

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000224635 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224635	ENST00000422519.2	n.1693-2615A>G		intron_variant	Intron 1 of 2	2

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

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0929

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.209

Alfa AF: 0.183 Hom.: 1386

Bravo AF: 0.224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1739646; hg19: chr20-37037584;