rs782054

Variant names:

• chr7-134434476-G-A
• rs782054

Your query was ambiguous. Multiple possible variants found:

• chr7-134434476-G-A
• chr7-134434476-G-C
• chr7-134434476-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.762 AC: 31582 AN: 41466

American (AMR) AF: 0.806 AC: 12323 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2298 AN: 3472

East Asian (EAS) AF: 0.936 AC: 4843 AN: 5174

South Asian (SAS) AF: 0.837 AC: 4032 AN: 4820

European-Finnish (FIN) AF: 0.786 AC: 8324 AN: 10590

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.771 AC: 52446 AN: 67992

Other (OTH) AF: 0.746 AC: 1574 AN: 2110

Alfa AF: 0.767 Hom.: 15563

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs782054; hg19: chr7-134119228;