rs4510766

Variant names:

• chr7-107852344-A-G
• rs4510766

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 0.364 in 152,174 control chromosomes in the GnomAD database, including 11,407 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 0.36 (11407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 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: 0.364 AC: 55418 AN: 152056 Hom.: 11401 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.364 AC: 55423 AN: 152174 Hom.: 11407 Cov.: 32 AF XY: 0.366 AC XY: 27220 AN XY: 74390

African (AFR) AF: 0.166 AC: 6874 AN: 41532

American (AMR) AF: 0.398 AC: 6090 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1619 AN: 3472

East Asian (EAS) AF: 0.529 AC: 2738 AN: 5178

South Asian (SAS) AF: 0.320 AC: 1543 AN: 4826

European-Finnish (FIN) AF: 0.456 AC: 4825 AN: 10584

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.447 AC: 30366 AN: 67980

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.419 Hom.: 37010

Bravo AF: 0.355

Asia WGS AF: 0.413 AC: 1435 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	5.6
DANN	Benign	0.85
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs4510766; hg19: chr7-107492789;