7-52099689-T-G

Variant names:

• chr7-52099689-T-G
• rs6965611

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 0.202 in 152,130 control chromosomes in the GnomAD database, including 3,834 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 0.20 (3834 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 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: 0.202 AC: 30700 AN: 152012 Hom.: 3838 Cov.: 32

Gnomad AFR AF: 0.0591

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.202 AC: 30699 AN: 152130 Hom.: 3834 Cov.: 32 AF XY: 0.211 AC XY: 15671 AN XY: 74360

African (AFR) AF: 0.0591 AC: 2457 AN: 41542

American (AMR) AF: 0.243 AC: 3710 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 960 AN: 3468

East Asian (EAS) AF: 0.445 AC: 2300 AN: 5166

South Asian (SAS) AF: 0.309 AC: 1491 AN: 4822

European-Finnish (FIN) AF: 0.310 AC: 3269 AN: 10560

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15748 AN: 67978

Other (OTH) AF: 0.212 AC: 448 AN: 2114

Alfa AF: 0.219 Hom.: 13351

Bravo AF: 0.191

Asia WGS AF: 0.314 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	4.2
DANN	Benign	0.81
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs6965611; hg19: chr7-52167385;