5-6266610-A-G

Variant names:

• chr5-6266610-A-G
• rs3846569
• ENST00000723274.1:n.107+19891T>C

Variant summary

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

The ENST00000723274.1(ENSG00000294384):​n.107+19891T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,332 control chromosomes in the GnomAD database, including 61,305 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 0.90 (61305 hom., cov: 35)
• Consequence: ENSG00000294384 ENST00000723274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 2 publications found

Genes affected

ENSG00000294384 (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 (NFE) allele frequency at 95% confidence interval = 0.911 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
ENSG00000294384	ENST00000723274.1	n.107+19891T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136487 AN: 152214 Hom.: 61264 Cov.: 35

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.897 AC: 136585 AN: 152332 Hom.: 61305 Cov.: 35 AF XY: 0.899 AC XY: 66941 AN XY: 74494

African (AFR) AF: 0.862 AC: 35849 AN: 41570

American (AMR) AF: 0.876 AC: 13409 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2929 AN: 3472

East Asian (EAS) AF: 0.858 AC: 4453 AN: 5188

South Asian (SAS) AF: 0.906 AC: 4373 AN: 4828

European-Finnish (FIN) AF: 0.964 AC: 10242 AN: 10628

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62355 AN: 68024

Other (OTH) AF: 0.876 AC: 1854 AN: 2116

Alfa AF: 0.901 Hom.: 157255

Bravo AF: 0.885

Asia WGS AF: 0.866 AC: 3010 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	0.75
DANN	Benign	0.27
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs3846569; hg19: chr5-6266723;