rs782054

Positions:

• chr7-134434476-G-A
• chr7-134434476-G-C
• chr7-134434476-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 0.777 in 152,110 control chromosomes in the GnomAD database, including 46,147 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 0.78 (46147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118102 AN: 151992 Hom.: 46103 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.777 AC: 118203 AN: 152110 Hom.: 46147 Cov.: 32 AF XY: 0.779 AC XY: 57929 AN XY: 74376

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.786

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.746

Alfa AF: 0.770 Hom.: 9399

Bravo AF: 0.775

Asia WGS AF: 0.861 AC: 2993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs782054; hg19: chr7-134119228;