5-4198432-T-C

Variant names:

• chr5-4198432-T-C
• rs6555262
• ENST00000762810.1:n.910T>C

Variant summary

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

The ENST00000762810.1(ENSG00000299354):​n.910T>C 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 0.938 in 152,120 control chromosomes in the GnomAD database, including 67,087 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 0.94 (67087 hom., cov: 30)
• Consequence: ENSG00000299354 ENST00000762810.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 2 publications found

Genes affected

ENSG00000299354 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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
ENSG00000299354	ENST00000762810.1	n.910T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142626 AN: 152002 Hom.: 67053 Cov.: 30

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.938 AC: 142711 AN: 152120 Hom.: 67087 Cov.: 30 AF XY: 0.939 AC XY: 69851 AN XY: 74358

African (AFR) AF: 0.884 AC: 36646 AN: 41454

American (AMR) AF: 0.958 AC: 14647 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3362 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5134 AN: 5164

South Asian (SAS) AF: 0.906 AC: 4368 AN: 4820

European-Finnish (FIN) AF: 0.985 AC: 10435 AN: 10598

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65000 AN: 68014

Other (OTH) AF: 0.930 AC: 1965 AN: 2114

Alfa AF: 0.946 Hom.: 10818

Bravo AF: 0.936

Asia WGS AF: 0.916 AC: 3186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.34
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6555262; hg19: chr5-4198545;