rs735240

Variant names:

• chr19-7748450-G-A
• rs735240

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 0.398 in 152,084 control chromosomes in the GnomAD database, including 12,479 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 0.40 (12479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 46 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60448 AN: 151966 Hom.: 12447 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.398 AC: 60543 AN: 152084 Hom.: 12479 Cov.: 32 AF XY: 0.395 AC XY: 29337 AN XY: 74328

African (AFR) AF: 0.315 AC: 13064 AN: 41474

American (AMR) AF: 0.483 AC: 7381 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1445 AN: 3468

East Asian (EAS) AF: 0.253 AC: 1311 AN: 5174

South Asian (SAS) AF: 0.335 AC: 1615 AN: 4818

European-Finnish (FIN) AF: 0.403 AC: 4256 AN: 10560

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.444 AC: 30215 AN: 67992

Other (OTH) AF: 0.411 AC: 869 AN: 2114

Alfa AF: 0.423 Hom.: 27731

Bravo AF: 0.402

Asia WGS AF: 0.324 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.99
DANN	Benign	0.17
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs735240; hg19: chr19-7813336;