rs742614

chr20-33894826-A-Gchr20-33894826-A-T

Variant summary

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

The variant allele was found at a frequency of 0.559 in 152,008 control chromosomes in the GnomAD database, including 24,319 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 0.56 (24319 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84910 AN: 151890 Hom.: 24296 Cov.: 31

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.559 AC: 84976 AN: 152008 Hom.: 24319 Cov.: 31 AF XY: 0.551 AC XY: 40978 AN XY: 74320

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.590

Alfa AF: 0.495 Hom.: 4343

Bravo AF: 0.567

Asia WGS AF: 0.487 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.50
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs742614; hg19: chr20-32482632;