chr5-73489759-T-C

Position:

• chr5-73489759-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 127 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0103

Gnomad4 AMR AF: 0.0322

Gnomad4 ASJ AF: 0.0693

Gnomad4 EAS AF: 0.000243

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.0404

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.0451

Alfa AF: 0.0410 Hom.: 36

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs347240; hg19: chr5-72785584;