chr19-44910109-T-C

Variant names:

• chr19-44910109-T-C
• rs1081106
• ENST00000623895.1:n.735T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000623895.1(ENSG00000280087):​n.735T>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 0.0705 in 152,124 control chromosomes in the GnomAD database, including 630 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 0.071 (630 hom., cov: 31)
  • Exomes 𝑓: 0.038 (0 hom.)
• Consequence: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 7 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).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0881 is higher than 0.05.

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.735T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10721 AN: 151980 Hom.: 630 Cov.: 31

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0598

Gnomad ASJ AF: 0.0875

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0900

Gnomad OTH AF: 0.0736

GnomAD4 exome AF: 0.0385 AC: 1 AN: 26 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 16

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0455 AC: 1 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0705 AC: 10727 AN: 152098 Hom.: 630 Cov.: 31 AF XY: 0.0754 AC XY: 5607 AN XY: 74356

African (AFR) AF: 0.0156 AC: 649 AN: 41528

American (AMR) AF: 0.0598 AC: 911 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0875 AC: 303 AN: 3464

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5160

South Asian (SAS) AF: 0.0407 AC: 196 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2214 AN: 10580

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0900 AC: 6119 AN: 67984

Other (OTH) AF: 0.0728 AC: 154 AN: 2114

Alfa AF: 0.0765 Hom.: 76

Bravo AF: 0.0569

Asia WGS AF: 0.0150 AC: 52 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	1.0
DANN	Benign	0.35
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1081106; hg19: chr19-45413366;