rs8112960

Variant names:

• chr19-21592569-C-T
• rs8112960
• ENST00000594927.2:n.1438G>A

Variant summary

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

The ENST00000594927.2(ENSG00000268240):​n.1438G>A 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 0.323 in 152,086 control chromosomes in the GnomAD database, including 8,171 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 0.32 (8168 hom., cov: 32)
  • Exomes 𝑓: 0.32 (3 hom.)
• Consequence: ENSG00000268240 ENST00000594927.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 29 publications found

Genes affected

ENSG00000268240 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929007	XR_001754044.3	n.374G>A		non_coding_transcript_exon_variant	Exon 2 of 4
LOC101929007	XR_002958421.2	n.553G>A		non_coding_transcript_exon_variant	Exon 3 of 5
LOC101929007	XR_007067174.1	n.374G>A		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268240	ENST00000594927.2	n.1438G>A		non_coding_transcript_exon_variant	Exon 1 of 2	1
ENSG00000268240	ENST00000789632.1	n.310G>A		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000268240	ENST00000789636.1	n.297G>A		non_coding_transcript_exon_variant	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49156 AN: 151896 Hom.: 8165 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.344

GnomAD4 exome AF: 0.319 AC: 23 AN: 72 Hom.: 3 Cov.: 0 AF XY: 0.310 AC XY: 18 AN XY: 58

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.167 AC: 1 AN: 6

European-Finnish (FIN) AF: 0.333 AC: 2 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.386 AC: 17 AN: 44

Other (OTH) AF: 0.200 AC: 2 AN: 10

GnomAD4 genome AF: 0.323 AC: 49174 AN: 152014 Hom.: 8168 Cov.: 32 AF XY: 0.326 AC XY: 24198 AN XY: 74286

African (AFR) AF: 0.256 AC: 10619 AN: 41460

American (AMR) AF: 0.367 AC: 5612 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1306 AN: 3464

East Asian (EAS) AF: 0.403 AC: 2069 AN: 5140

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4822

European-Finnish (FIN) AF: 0.353 AC: 3730 AN: 10564

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23188 AN: 67964

Other (OTH) AF: 0.340 AC: 718 AN: 2114

Alfa AF: 0.336 Hom.: 27192

Bravo AF: 0.323

Asia WGS AF: 0.289 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.33
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs8112960; hg19: chr19-21775371;