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. The variant received -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
• Publications: 36 publications found

Genes affected

ENSG00000280087 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 65 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623895.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000280087	ENST00000623895.1	TSL:6	n.324A>C		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 0.0599 AC: 40 AN: 668

American (AMR) AF: 0.0159 AC: 49 AN: 3088

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 30 AN: 868

East Asian (EAS) AF: 0.00111 AC: 2 AN: 1804

South Asian (SAS) AF: 0.0192 AC: 126 AN: 6564

European-Finnish (FIN) AF: 0.0213 AC: 42 AN: 1974

Middle Eastern (MID) AF: 0.0234 AC: 3 AN: 128

European-Non Finnish (NFE) AF: 0.0269 AC: 717 AN: 26620

Other (OTH) AF: 0.0253 AC: 54 AN: 2132

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

African (AFR) AF: 0.0479 AC: 1975 AN: 41258

American (AMR) AF: 0.0137 AC: 208 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0310 AC: 107 AN: 3450

East Asian (EAS) AF: 0.00237 AC: 12 AN: 5060

South Asian (SAS) AF: 0.0261 AC: 125 AN: 4788

European-Finnish (FIN) AF: 0.0206 AC: 217 AN: 10534

Middle Eastern (MID) AF: 0.0208 AC: 6 AN: 288

European-Non Finnish (NFE) AF: 0.0259 AC: 1754 AN: 67764

Other (OTH) AF: 0.0214 AC: 45 AN: 2104

Alfa AF: 0.149 Hom.: 1409

Bravo AF: 0.0299

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1081105; hg19: chr19-45412955;