rs7514121

Variant names:

• chr1-162030642-G-A
• rs7514121

Your query was ambiguous. Multiple possible variants found:

• chr1-162030642-G-A
• chr1-162030642-G-C
• chr1-162030642-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;