5-111137830-A-T

Variant names:

• chr5-111137830-A-T
• rs417670
• ENST00000762371.1:n.369-1500T>A

Variant summary

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

The ENST00000762371.1(ENSG00000299289):​n.369-1500T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,138 control chromosomes in the GnomAD database, including 36,317 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 0.68 (36317 hom., cov: 33)
• Consequence: ENSG00000299289 ENST00000762371.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 3 publications found

Genes affected

ENSG00000299289 (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 = 0.934 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
ENSG00000299289	ENST00000762371.1	n.369-1500T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103940 AN: 152020 Hom.: 36289 Cov.: 33

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.684 AC: 104026 AN: 152138 Hom.: 36317 Cov.: 33 AF XY: 0.694 AC XY: 51616 AN XY: 74390

African (AFR) AF: 0.765 AC: 31731 AN: 41498

American (AMR) AF: 0.670 AC: 10227 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2132 AN: 3470

East Asian (EAS) AF: 0.956 AC: 4953 AN: 5182

South Asian (SAS) AF: 0.883 AC: 4259 AN: 4822

European-Finnish (FIN) AF: 0.706 AC: 7476 AN: 10586

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41142 AN: 67996

Other (OTH) AF: 0.668 AC: 1406 AN: 2104

Alfa AF: 0.649 Hom.: 3836

Bravo AF: 0.677

Asia WGS AF: 0.873 AC: 3037 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	1.4
DANN	Benign	0.43
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs417670; hg19: chr5-110473528;