chr7-53980332-A-G

Variant names:

• chr7-53980332-A-G
• rs7789754

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 0.1 in 152,186 control chromosomes in the GnomAD database, including 812 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 (812 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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: 0.100 AC: 15209 AN: 152068 Hom.: 813 Cov.: 32

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.100 AC: 15222 AN: 152186 Hom.: 812 Cov.: 32 AF XY: 0.102 AC XY: 7619 AN XY: 74414

African (AFR) AF: 0.0670 AC: 2784 AN: 41526

American (AMR) AF: 0.109 AC: 1671 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1009 AN: 5162

South Asian (SAS) AF: 0.156 AC: 752 AN: 4818

European-Finnish (FIN) AF: 0.131 AC: 1390 AN: 10608

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6802 AN: 68012

Other (OTH) AF: 0.0985 AC: 208 AN: 2112

Alfa AF: 0.0955 Hom.: 972

Bravo AF: 0.0963

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7789754; hg19: chr7-54048025;