rs4861775

Variant names:

• chr4-179395497-A-C
• rs4861775
• ENST00000512036.1:n.112-5408T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-179395497-A-C
• chr4-179395497-A-T

Variant summary

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

The ENST00000512036.1(ENSG00000250993):​n.112-5408T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,128 control chromosomes in the GnomAD database, including 2,330 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 0.16 (2330 hom., cov: 32)
• Consequence: ENSG00000250993 ENST00000512036.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• Publications: 3 publications found

Genes affected

ENSG00000250993 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 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
ENSG00000250993	ENST00000512036.1	n.112-5408T>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23898 AN: 152012 Hom.: 2328 Cov.: 32

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.157 AC: 23909 AN: 152128 Hom.: 2330 Cov.: 32 AF XY: 0.157 AC XY: 11694 AN XY: 74380

African (AFR) AF: 0.0460 AC: 1912 AN: 41560

American (AMR) AF: 0.199 AC: 3037 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3468

East Asian (EAS) AF: 0.318 AC: 1638 AN: 5158

South Asian (SAS) AF: 0.124 AC: 597 AN: 4822

European-Finnish (FIN) AF: 0.195 AC: 2057 AN: 10534

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13409 AN: 67978

Other (OTH) AF: 0.183 AC: 386 AN: 2112

Alfa AF: 0.179 Hom.: 6812

Bravo AF: 0.155

Asia WGS AF: 0.194 AC: 671 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.6
DANN	Benign	0.88
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs4861775; hg19: chr4-180316651;