rs1081105

Positions:

• chr19-44909698-A-C
• chr19-44909698-A-G

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 0.0282 in 195,214 control chromosomes in the GnomAD database, including 89 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 0.029 (65 hom., cov: 32)
  • Exomes 𝑓: 0.024 (24 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0294 (4450/151368) while in subpopulation AFR AF= 0.0479 (1975/41258). AF 95% confidence interval is 0.0461. There are 65 homozygotes in gnomad4. There are 2157 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 65 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: 0.0294 AC: 4447 AN: 151250 Hom.: 64 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0138

Gnomad ASJ AF: 0.0310

Gnomad EAS AF: 0.00237

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0206

Gnomad MID AF: 0.0227

Gnomad NFE AF: 0.0259

Gnomad OTH AF: 0.0216

GnomAD4 exome AF: 0.0242 AC: 1063 AN: 43846 Hom.: 24 Cov.: 0 AF XY: 0.0230 AC XY: 533 AN XY: 23218

Gnomad4 AFR exome AF: 0.0599

Gnomad4 AMR exome AF: 0.0159

Gnomad4 ASJ exome AF: 0.0346

Gnomad4 EAS exome AF: 0.00111

Gnomad4 SAS exome AF: 0.0192

Gnomad4 FIN exome AF: 0.0213

Gnomad4 NFE exome AF: 0.0269

Gnomad4 OTH exome AF: 0.0253

GnomAD4 genome AF: 0.0294 AC: 4450 AN: 151368 Hom.: 65 Cov.: 32 AF XY: 0.0292 AC XY: 2157 AN XY: 73972

Gnomad4 AFR AF: 0.0479

Gnomad4 AMR AF: 0.0137

Gnomad4 ASJ AF: 0.0310

Gnomad4 EAS AF: 0.00237

Gnomad4 SAS AF: 0.0261

Gnomad4 FIN AF: 0.0206

Gnomad4 NFE AF: 0.0259

Gnomad4 OTH AF: 0.0214

Alfa AF: 0.153 Hom.: 1409

Bravo AF: 0.0299

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1081105; hg19: chr19-45412955;