rs2796146

Variant names:

• chr1-234792214-G-A
• rs2796146
• ENST00000761072.1:n.111-11800C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-234792214-G-A
• chr1-234792214-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000761072.1(ENSG00000299147):​n.111-11800C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.34 (2 hom., cov: 37)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000299147 ENST00000761072.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 0 publications found

Genes affected

ENSG00000299147 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904557	XR_007066954.1	n.669+1518C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299147	ENST00000761072.1	n.111-11800C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 33263 AN: 98352 Hom.: 2 Cov.: 37

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.384

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.340

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.338 AC: 33274 AN: 98448 Hom.: 2 Cov.: 37 AF XY: 0.333 AC XY: 15915 AN XY: 47792

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.220 AC: 5719 AN: 26042

American (AMR) AF: 0.370 AC: 3701 AN: 10010

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 924 AN: 2288

East Asian (EAS) AF: 0.220 AC: 793 AN: 3600

South Asian (SAS) AF: 0.393 AC: 1253 AN: 3192

European-Finnish (FIN) AF: 0.368 AC: 2568 AN: 6984

Middle Eastern (MID) AF: 0.378 AC: 62 AN: 164

European-Non Finnish (NFE) AF: 0.397 AC: 17548 AN: 44204

Other (OTH) AF: 0.341 AC: 467 AN: 1368

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.258 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.72
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2796146; hg19: chr1-234927961;