1-234792214-G-A

Variant names:

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761072.1. 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
	ENSG00000299147	ENST00000761072.1		n.111-11800C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2796146;

hg19: chr1-234927961;