rs12530731

Positions:

• chr7-73944846-G-A
• chr7-73944846-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 0.305 in 151,946 control chromosomes in the GnomAD database, including 8,680 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 0.30 (8680 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 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: 0.305 AC: 46235 AN: 151830 Hom.: 8640 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.305 AC: 46331 AN: 151946 Hom.: 8680 Cov.: 32 AF XY: 0.311 AC XY: 23102 AN XY: 74272

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.269

Alfa AF: 0.237 Hom.: 3613

Bravo AF: 0.321

Asia WGS AF: 0.465 AC: 1616 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
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: rs12530731; hg19: chr7-73359176;