5-4198323-T-C

Variant names:

• chr5-4198323-T-C
• rs6555261
• ENST00000762810.1:n.801T>C

Variant summary

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

The ENST00000762810.1(ENSG00000299354):​n.801T>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 0.925 in 152,226 control chromosomes in the GnomAD database, including 65,396 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 0.92 (65396 hom., cov: 32)
• Consequence: ENSG00000299354 ENST00000762810.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735
• Publications: 3 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=-0.91).
• 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.801T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140719 AN: 152106 Hom.: 65368 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.925 AC: 140799 AN: 152226 Hom.: 65396 Cov.: 32 AF XY: 0.926 AC XY: 68940 AN XY: 74432

African (AFR) AF: 0.839 AC: 34820 AN: 41516

American (AMR) AF: 0.954 AC: 14600 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3363 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5129 AN: 5160

South Asian (SAS) AF: 0.901 AC: 4345 AN: 4824

European-Finnish (FIN) AF: 0.985 AC: 10443 AN: 10606

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

European-Non Finnish (NFE) AF: 0.955 AC: 64999 AN: 68028

Other (OTH) AF: 0.920 AC: 1944 AN: 2114

Alfa AF: 0.944 Hom.: 95161

Bravo AF: 0.921

Asia WGS AF: 0.913 AC: 3175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.41
DANN	Benign	0.35
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs6555261; hg19: chr5-4198436;