chr4-87975096-G-T

Variant names:

• chr4-87975096-G-T
• rs2853744
• ENST00000662475.1:n.1074C>A

Variant summary

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

The ENST00000662475.1(ENSG00000286618):​n.1074C>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 0.14 in 152,196 control chromosomes in the GnomAD database, including 2,166 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 0.14 (2166 hom., cov: 33)
• Consequence: ENSG00000286618 ENST00000662475.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 23 publications found

Genes affected

ENSG00000286618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 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
ENSG00000286618	ENST00000662475.1	n.1074C>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21344 AN: 152078 Hom.: 2163 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.140 AC: 21372 AN: 152196 Hom.: 2166 Cov.: 33 AF XY: 0.146 AC XY: 10828 AN XY: 74414

African (AFR) AF: 0.257 AC: 10652 AN: 41498

American (AMR) AF: 0.100 AC: 1532 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3470

East Asian (EAS) AF: 0.365 AC: 1886 AN: 5170

South Asian (SAS) AF: 0.153 AC: 740 AN: 4824

European-Finnish (FIN) AF: 0.132 AC: 1396 AN: 10594

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0628 AC: 4272 AN: 68036

Other (OTH) AF: 0.144 AC: 304 AN: 2112

Alfa AF: 0.104 Hom.: 1970

Bravo AF: 0.144

Asia WGS AF: 0.239 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.56
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2853744; hg19: chr4-88896248;