rs2172797

chr4-74518755-G-Achr4-74518755-G-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 0.0746 in 152,194 control chromosomes in the GnomAD database, including 500 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 0.075 (500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 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: 0.0744 AC: 11316 AN: 152076 Hom.: 488 Cov.: 32

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.0793

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0523

Gnomad OTH AF: 0.0701

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

GnomAD4 genome AF: 0.0746 AC: 11353 AN: 152194 Hom.: 500 Cov.: 32 AF XY: 0.0780 AC XY: 5808 AN XY: 74424

Gnomad4 AFR AF: 0.0971

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0581

Gnomad4 NFE AF: 0.0523

Gnomad4 OTH AF: 0.0760

Alfa AF: 0.0223 Hom.: 9

Bravo AF: 0.0756

Asia WGS AF: 0.146 AC: 509 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	0.11
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2172797; hg19: chr4-75384472;