rs601419

Variant names:

• chr11-74483605-G-A
• rs601419
• ENST00000533008.1:n.155-572G>A

Variant summary

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

The ENST00000533008.1(ENSG00000254631):​n.155-572G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,004 control chromosomes in the GnomAD database, including 30,188 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 0.62 (30188 hom., cov: 32)
• Consequence: ENSG00000254631 ENST00000533008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 1 publications found

Genes affected

ENSG00000254631 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 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
ENSG00000254631	ENST00000533008.1	n.155-572G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94468 AN: 151884 Hom.: 30197 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.622 AC: 94488 AN: 152004 Hom.: 30188 Cov.: 32 AF XY: 0.616 AC XY: 45781 AN XY: 74298

African (AFR) AF: 0.472 AC: 19538 AN: 41424

American (AMR) AF: 0.593 AC: 9053 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2401 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3370 AN: 5174

South Asian (SAS) AF: 0.532 AC: 2567 AN: 4826

European-Finnish (FIN) AF: 0.672 AC: 7097 AN: 10554

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.713 AC: 48491 AN: 67970

Other (OTH) AF: 0.626 AC: 1323 AN: 2112

Alfa AF: 0.689 Hom.: 53450

Bravo AF: 0.612

Asia WGS AF: 0.532 AC: 1846 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.59
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs601419; hg19: chr11-74194650;