4-44100-T-C

Variant names:

• chr4-44100-T-C
• rs1572075
• ENST00000800880.1:n.499A>G

Variant summary

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

The ENST00000800880.1(ENSG00000304187):​n.499A>G 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 0.00357 in 133,726 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0036 (0 hom., cov: 35)
• Consequence: ENSG00000304187 ENST00000800880.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 0 publications found

Genes affected

ENSG00000304187 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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
ENSG00000304187	ENST00000800880.1	n.499A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000304187	ENST00000800879.1	n.120+7218A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.00358 AC: 478 AN: 133624 Hom.: 0 Cov.: 35

Gnomad AFR AF: 0.00230

Gnomad AMI AF: 0.00253

Gnomad AMR AF: 0.00225

Gnomad ASJ AF: 0.00370

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00612

Gnomad FIN AF: 0.00684

Gnomad MID AF: 0.00746

Gnomad NFE AF: 0.00427

Gnomad OTH AF: 0.00546

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

GnomAD4 genome AF: 0.00357 AC: 478 AN: 133726 Hom.: 0 Cov.: 35 AF XY: 0.00350 AC XY: 228 AN XY: 65208

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

African (AFR) AF: 0.00226 AC: 85 AN: 37552

American (AMR) AF: 0.00224 AC: 31 AN: 13824

Ashkenazi Jewish (ASJ) AF: 0.00370 AC: 11 AN: 2972

East Asian (EAS) AF: 0.00 AC: 0 AN: 5006

South Asian (SAS) AF: 0.00638 AC: 26 AN: 4078

European-Finnish (FIN) AF: 0.00684 AC: 61 AN: 8920

Middle Eastern (MID) AF: 0.00800 AC: 2 AN: 250

European-Non Finnish (NFE) AF: 0.00427 AC: 250 AN: 58488

Other (OTH) AF: 0.00542 AC: 10 AN: 1846

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00666 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.67
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1572075; hg19: chr4-44101; COSMIC: COSV74114096;