chr7-51923643-G-A

Variant names:

• chr7-51923643-G-A
• rs7783471

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 0.0662 in 152,262 control chromosomes in the GnomAD database, including 375 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 0.066 (375 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.077 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: 0.0662 AC: 10079 AN: 152144 Hom.: 375 Cov.: 33

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0491

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.0683

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

GnomAD4 genome AF: 0.0662 AC: 10084 AN: 152262 Hom.: 375 Cov.: 33 AF XY: 0.0656 AC XY: 4887 AN XY: 74454

African (AFR) AF: 0.0793 AC: 3295 AN: 41554

American (AMR) AF: 0.0490 AC: 749 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0504 AC: 175 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0514 AC: 248 AN: 4828

European-Finnish (FIN) AF: 0.0779 AC: 826 AN: 10608

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0671 AC: 4562 AN: 68018

Other (OTH) AF: 0.0676 AC: 143 AN: 2116

Alfa AF: 0.0663 Hom.: 705

Bravo AF: 0.0652

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
DANN	Benign	0.45
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs7783471; hg19: chr7-51991339;