rs2749817

Positions:

• chr20-23078618-T-C
• chr20-23078618-T-G

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 0.566 in 152,106 control chromosomes in the GnomAD database, including 26,112 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 0.57 (26112 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86101 AN: 151988 Hom.: 26094 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.566 AC: 86159 AN: 152106 Hom.: 26112 Cov.: 32 AF XY: 0.562 AC XY: 41773 AN XY: 74376

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.632

Alfa AF: 0.643 Hom.: 18025

Bravo AF: 0.573

Asia WGS AF: 0.696 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2749817; hg19: chr20-23059255;