rs10517128

chr4-27779759-G-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 0.0191 in 152,258 control chromosomes in the GnomAD database, including 27 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 0.019 (27 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0191 (2903/152258) while in subpopulation NFE AF= 0.0219 (1493/68024). AF 95% confidence interval is 0.021. There are 27 homozygotes in gnomad4. There are 1391 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 27 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0191 AC: 2903 AN: 152140 Hom.: 27 Cov.: 32

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0206

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00766

Gnomad FIN AF: 0.00782

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0219

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0191 AC: 2903 AN: 152258 Hom.: 27 Cov.: 32 AF XY: 0.0187 AC XY: 1391 AN XY: 74436

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.0206

Gnomad4 ASJ AF: 0.0473

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00788

Gnomad4 FIN AF: 0.00782

Gnomad4 NFE AF: 0.0219

Gnomad4 OTH AF: 0.0298

Alfa AF: 0.0224 Hom.: 4

Bravo AF: 0.0204

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.3
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517128; hg19: chr4-27781381;