1-96038950-C-T

Variant names:

• chr1-96038950-C-T
• rs10518592

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 0.012 in 152,210 control chromosomes in the GnomAD database, including 31 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 0.012 (31 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.012 (1834/152210) while in subpopulation AFR AF= 0.0319 (1325/41526). AF 95% confidence interval is 0.0305. There are 31 homozygotes in gnomad4. There are 927 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 31 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: 0.0121 AC: 1833 AN: 152092 Hom.: 31 Cov.: 32

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00616

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.0282

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00263

Gnomad OTH AF: 0.0139

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

GnomAD4 genome AF: 0.0120 AC: 1834 AN: 152210 Hom.: 31 Cov.: 32 AF XY: 0.0125 AC XY: 927 AN XY: 74418

Gnomad4 AFR AF: 0.0319

Gnomad4 AMR AF: 0.00609

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.00541

Gnomad4 SAS AF: 0.0280

Gnomad4 FIN AF: 0.000189

Gnomad4 NFE AF: 0.00263

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.00204 Hom.: 0

Bravo AF: 0.0130

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518592; hg19: chr1-96504506;