rs4650707

chr1-175153430-A-Gchr1-175153430-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 0.975 in 152,366 control chromosomes in the GnomAD database, including 72,456 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 0.98 (72456 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 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: 0.975 AC: 148463 AN: 152248 Hom.: 72398 Cov.: 33

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.992

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.961

Gnomad OTH AF: 0.976

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

GnomAD4 genome AF: 0.975 AC: 148580 AN: 152366 Hom.: 72456 Cov.: 33 AF XY: 0.977 AC XY: 72824 AN XY: 74512

Gnomad4 AFR AF: 0.993

Gnomad4 AMR AF: 0.971

Gnomad4 ASJ AF: 0.982

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.992

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.961

Gnomad4 OTH AF: 0.976

Alfa AF: 0.972 Hom.: 10516

Bravo AF: 0.974

Asia WGS AF: 0.992 AC: 3450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.8
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4650707; hg19: chr1-175122566;