rs1081105

Variant names:

• chr19-44909698-A-C
• rs1081105
• ENST00000623895.1:n.324A>C

Your query was ambiguous. Multiple possible variants found:

• 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 ENST00000623895.1(ENSG00000280087):​n.324A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849

Genes affected

ENSG00000280087 (HGNC:):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000280087	ENST00000623895.1	n.324A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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;