rs1472272

Variant names:

• chr7-98483662-T-C
• rs1472272

Your query was ambiguous. Multiple possible variants found:

• chr7-98483662-T-C
• chr7-98483662-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 0.186 in 151,972 control chromosomes in the GnomAD database, including 2,872 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 0.19 (2872 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 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: 0.186 AC: 28274 AN: 151854 Hom.: 2871 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.186 AC: 28298 AN: 151972 Hom.: 2872 Cov.: 31 AF XY: 0.188 AC XY: 13952 AN XY: 74276

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.190

Alfa AF: 0.120 Hom.: 339

Bravo AF: 0.189

Asia WGS AF: 0.236 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.67
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1472272; hg19: chr7-98112974;