rs574383

Variant names:

• chr11-118702959-T-C
• rs574383
• ENST00000646572.2:n.230-1649T>C

Variant summary

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

The ENST00000646572.2(ENSG00000255422):​n.230-1649T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,936 control chromosomes in the GnomAD database, including 9,133 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 0.34 (9133 hom., cov: 31)
• Consequence: ENSG00000255422 ENST00000646572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466
• Publications: 8 publications found

Genes affected

ENSG00000255422 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646572.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255422	ENST00000646572.2		n.230-1649T>C		intron	N/A
	ENSG00000255422	ENST00000702882.1		n.230-1720T>C		intron	N/A
	ENSG00000255422	ENST00000775653.1		n.230+2316T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51613 AN: 151818 Hom.: 9116 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.340 AC: 51676 AN: 151936 Hom.: 9133 Cov.: 31 AF XY: 0.339 AC XY: 25134 AN XY: 74244

African (AFR) AF: 0.350 AC: 14512 AN: 41448

American (AMR) AF: 0.473 AC: 7202 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1161 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1946 AN: 5162

South Asian (SAS) AF: 0.182 AC: 876 AN: 4824

European-Finnish (FIN) AF: 0.302 AC: 3183 AN: 10534

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21549 AN: 67944

Other (OTH) AF: 0.345 AC: 726 AN: 2106

Alfa AF: 0.336 Hom.: 1110

Bravo AF: 0.360

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.80
PhyloP100		0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs574383;

hg19: chr11-118573668;