rs847964

Positions:

• chr7-12453831-G-A
• chr7-12453831-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 0.102 in 151,942 control chromosomes in the GnomAD database, including 985 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 0.10 (985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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: 0.102 AC: 15540 AN: 151824 Hom.: 978 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0943

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0773

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.102 AC: 15568 AN: 151942 Hom.: 985 Cov.: 32 AF XY: 0.0996 AC XY: 7392 AN XY: 74248

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0843

Gnomad4 ASJ AF: 0.0943

Gnomad4 EAS AF: 0.0613

Gnomad4 SAS AF: 0.0424

Gnomad4 FIN AF: 0.0389

Gnomad4 NFE AF: 0.0773

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0897 Hom.: 89

Bravo AF: 0.111

Asia WGS AF: 0.0620 AC: 216 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.085

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs847964; hg19: chr7-12493457;