rs347240

Variant names:

• chr5-73489759-T-C
• rs347240

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 0.0352 in 139,054 control chromosomes in the GnomAD database, including 127 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 0.035 (127 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.725
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0352 (4893/139054) while in subpopulation NFE AF = 0.0475 (3221/67800). AF 95% confidence interval is 0.0461. There are 127 homozygotes in GnomAd4. There are 2319 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 127 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: 0.0352 AC: 4893 AN: 138964 Hom.: 127 Cov.: 33

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.0232

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.0693

Gnomad EAS AF: 0.000242

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.0449

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0352 AC: 4893 AN: 139054 Hom.: 127 Cov.: 33 AF XY: 0.0341 AC XY: 2319 AN XY: 68032

African (AFR) AF: 0.0103 AC: 312 AN: 30416

American (AMR) AF: 0.0322 AC: 479 AN: 14898

Ashkenazi Jewish (ASJ) AF: 0.0693 AC: 239 AN: 3450

East Asian (EAS) AF: 0.000243 AC: 1 AN: 4118

South Asian (SAS) AF: 0.0201 AC: 95 AN: 4726

European-Finnish (FIN) AF: 0.0404 AC: 422 AN: 10456

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0475 AC: 3221 AN: 67800

Other (OTH) AF: 0.0451 AC: 90 AN: 1994

Alfa AF: 0.0322 Hom.: 55

Bravo AF: 0.0303

Asia WGS AF: 0.0120 AC: 41 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	8.6
DANN	Benign	0.43
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs347240; hg19: chr5-72785584;