chr7-53985565-A-G

Variant names:

• chr7-53985565-A-G
• rs10499725

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0155 in 152,318 control chromosomes in the GnomAD database, including 27 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 0.015 (27 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0155 (2356/152318) while in subpopulation NFE AF = 0.018 (1223/68018). AF 95% confidence interval is 0.0171. There are 27 homozygotes in GnomAd4. There are 1119 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 27 gene

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: 0.0155 AC: 2358 AN: 152202 Hom.: 27 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0177

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.00791

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0248

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

GnomAD4 genome AF: 0.0155 AC: 2356 AN: 152318 Hom.: 27 Cov.: 32 AF XY: 0.0150 AC XY: 1119 AN XY: 74484

African (AFR) AF: 0.0129 AC: 535 AN: 41578

American (AMR) AF: 0.0176 AC: 270 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.00435 AC: 21 AN: 4826

European-Finnish (FIN) AF: 0.00791 AC: 84 AN: 10626

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0180 AC: 1223 AN: 68018

Other (OTH) AF: 0.0246 AC: 52 AN: 2114

Alfa AF: 0.0148 Hom.: 2

Bravo AF: 0.0170

Asia WGS AF: 0.00318 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.74
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10499725; hg19: chr7-54053258;