rs7259340

Variant names:

• chr19-43682501-C-A
• rs7259340

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 0.295 in 149,792 control chromosomes in the GnomAD database, including 6,871 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 0.29 (6871 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 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: 0.295 AC: 44189 AN: 149722 Hom.: 6877 Cov.: 29

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.400

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.295 AC: 44175 AN: 149792 Hom.: 6871 Cov.: 29 AF XY: 0.287 AC XY: 21012 AN XY: 73102

African (AFR) AF: 0.285 AC: 11656 AN: 40896

American (AMR) AF: 0.234 AC: 3514 AN: 15000

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1504 AN: 3468

East Asian (EAS) AF: 0.0461 AC: 235 AN: 5094

South Asian (SAS) AF: 0.250 AC: 1187 AN: 4754

European-Finnish (FIN) AF: 0.258 AC: 2505 AN: 9712

Middle Eastern (MID) AF: 0.395 AC: 113 AN: 286

European-Non Finnish (NFE) AF: 0.332 AC: 22409 AN: 67596

Other (OTH) AF: 0.307 AC: 640 AN: 2084

Alfa AF: 0.319 Hom.: 10411

Bravo AF: 0.291

Asia WGS AF: 0.172 AC: 597 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.26
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7259340; hg19: chr19-44186653;