rs7417366

Positions:

• chr1-168494349-A-G
• chr1-168494349-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000422253.1(ENSG00000228697):​n.58-225T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,100 control chromosomes in the GnomAD database, including 8,612 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 0.31 (8612 hom., cov: 32)
• Consequence: ENSG00000228697 ENST00000422253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.952

Genes affected

ENSG00000228697 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928565	NR_125956.2	n.54-225T>C		intron_variant
LOC101928565	NR_176056.1	n.54-162T>C		intron_variant
LOC101928565	NR_176057.1	n.54-206T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000228697	ENST00000422253.1	n.58-225T>C		intron_variant		1
ENSG00000228697	ENST00000636459.1	n.99-206T>C		intron_variant		5
ENSG00000228697	ENST00000650143.1	n.56+1239T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47078 AN: 151986 Hom.: 8610 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.310 AC: 47082 AN: 152100 Hom.: 8612 Cov.: 32 AF XY: 0.320 AC XY: 23831 AN XY: 74366

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.314

Alfa AF: 0.352 Hom.: 10950

Bravo AF: 0.304

Asia WGS AF: 0.455 AC: 1576 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	17
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7417366; hg19: chr1-168463587;