5-62199286-C-T

Variant names:

• chr5-62199286-C-T
• rs17366217
• ENST00000701665.2:n.89+42843G>A

Variant summary

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

The ENST00000701665.2(ENSG00000289916):​n.89+42843G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,170 control chromosomes in the GnomAD database, including 1,275 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 0.12 (1275 hom., cov: 32)
• Consequence: ENSG00000289916 ENST00000701665.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799
• Publications: 2 publications found

Genes affected

ENSG00000289916 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 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
ENSG00000289916	ENST00000701665.2	n.89+42843G>A		intron_variant	Intron 1 of 9
ENSG00000289916	ENST00000777173.1	n.131+42843G>A		intron_variant	Intron 1 of 4
ENSG00000289916	ENST00000777174.1	n.104+42843G>A		intron_variant	Intron 1 of 8

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18314 AN: 152052 Hom.: 1275 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0936

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.0350

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0566

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0985

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.120 AC: 18324 AN: 152170 Hom.: 1275 Cov.: 32 AF XY: 0.118 AC XY: 8763 AN XY: 74396

African (AFR) AF: 0.190 AC: 7889 AN: 41518

American (AMR) AF: 0.103 AC: 1578 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0723 AC: 251 AN: 3472

East Asian (EAS) AF: 0.0349 AC: 181 AN: 5182

South Asian (SAS) AF: 0.156 AC: 751 AN: 4820

European-Finnish (FIN) AF: 0.0566 AC: 601 AN: 10610

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0985 AC: 6698 AN: 67988

Other (OTH) AF: 0.117 AC: 248 AN: 2112

Alfa AF: 0.0889 Hom.: 301

Bravo AF: 0.125

Asia WGS AF: 0.0850 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	13
DANN	Benign	0.53
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs17366217; hg19: chr5-61495113;