rs4650707

Variant names:

• chr1-175153430-A-G
• rs4650707

Your query was ambiguous. Multiple possible variants found:

• chr1-175153430-A-G
• chr1-175153430-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;