rs1972603

Variant names:

• chr18-29149852-T-A
• rs1972603

Your query was ambiguous. Multiple possible variants found:

• chr18-29149852-T-A
• chr18-29149852-T-C
• chr18-29149852-T-G

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 0.456 in 151,580 control chromosomes in the GnomAD database, including 18,660 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 0.46 (18660 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 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: 0.456 AC: 69041 AN: 151462 Hom.: 18652 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.456 AC: 69069 AN: 151580 Hom.: 18660 Cov.: 31 AF XY: 0.452 AC XY: 33504 AN XY: 74046

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.556

Alfa AF: 0.512 Hom.: 2662

Bravo AF: 0.454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.53
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1972603; hg19: chr18-26729817;