5-34389754-T-C

Variant names:

• chr5-34389754-T-C
• rs1440423
• ENST00000806125.1:n.247+5116T>C

Variant summary

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

The ENST00000806125.1(ENSG00000304753):​n.247+5116T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.975 in 146,854 control chromosomes in the GnomAD database, including 69,856 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 0.97 (69856 hom., cov: 23)
• Consequence: ENSG00000304753 ENST00000806125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 2 publications found

Genes affected

ENSG00000304753 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 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
ENSG00000304753	ENST00000806125.1	n.247+5116T>C		intron_variant	Intron 1 of 3
ENSG00000304753	ENST00000806126.1	n.446-25575T>C		intron_variant	Intron 2 of 3
ENSG00000304753	ENST00000806127.1	n.266+5116T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.975 AC: 143050 AN: 146742 Hom.: 69816 Cov.: 23

Gnomad AFR AF: 0.963

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.981

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

GnomAD4 genome AF: 0.975 AC: 143141 AN: 146854 Hom.: 69856 Cov.: 23 AF XY: 0.972 AC XY: 69378 AN XY: 71360

African (AFR) AF: 0.962 AC: 37719 AN: 39196

American (AMR) AF: 0.930 AC: 13611 AN: 14634

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3405 AN: 3420

East Asian (EAS) AF: 0.847 AC: 4198 AN: 4956

South Asian (SAS) AF: 0.967 AC: 4429 AN: 4578

European-Finnish (FIN) AF: 0.998 AC: 10012 AN: 10032

Middle Eastern (MID) AF: 0.997 AC: 289 AN: 290

European-Non Finnish (NFE) AF: 0.997 AC: 66573 AN: 66804

Other (OTH) AF: 0.981 AC: 1997 AN: 2036

Alfa AF: 0.991 Hom.: 72503

Bravo AF: 0.969

Asia WGS AF: 0.913 AC: 3162 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.2
DANN	Benign	0.43
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs1440423; hg19: chr5-34389859;