rs7514121

chr1-162030642-G-Achr1-162030642-G-Cchr1-162030642-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 0.731 in 152,128 control chromosomes in the GnomAD database, including 41,380 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 0.73 (41380 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.806 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: 0.731 AC: 111108 AN: 152010 Hom.: 41370 Cov.: 33

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.731 AC: 111159 AN: 152128 Hom.: 41380 Cov.: 33 AF XY: 0.734 AC XY: 54635 AN XY: 74396

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.715

Alfa AF: 0.773 Hom.: 62912

Bravo AF: 0.723

Asia WGS AF: 0.675 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.1
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7514121; hg19: chr1-162000432;