rs302001

Variant names:

• chr1-37259347-G-A
• rs302001
• ENST00000655056.1:n.593+11109C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655056.1(ENSG00000223944):​n.593+11109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,250 control chromosomes in the GnomAD database, including 1,130 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 0.12 (1130 hom., cov: 32)
• Consequence: ENSG00000223944 ENST00000655056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

Genes affected

ENSG00000223944 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 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
ENSG00000223944	ENST00000655056.1	n.593+11109C>T		intron_variant	Intron 3 of 3
ENSG00000223944	ENST00000657513.1	n.257+11109C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17605 AN: 152132 Hom.: 1132 Cov.: 32

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.116 AC: 17615 AN: 152250 Hom.: 1130 Cov.: 32 AF XY: 0.114 AC XY: 8513 AN XY: 74442

Gnomad4 AFR AF: 0.0995

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.124

Alfa AF: 0.123 Hom.: 470

Bravo AF: 0.114

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0060
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs302001; hg19: chr1-37724948;