rs947425

Variant names:

• chr1-119320733-G-A
• rs947425
• ENST00000457719.1:n.341+6230C>T

Variant summary

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

The ENST00000457719.1(ENSG00000227712):​n.341+6230C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,100 control chromosomes in the GnomAD database, including 2,166 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 0.10 (2166 hom., cov: 32)
• Consequence: ENSG00000227712 ENST00000457719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

Genes affected

ENSG00000227712 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 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
ENSG00000227712	ENST00000457719.1	n.341+6230C>T		intron_variant	Intron 1 of 2	2
ENSG00000227712	ENST00000653227.1	n.287-2806C>T		intron_variant	Intron 2 of 2
ENSG00000227712	ENST00000655614.1	n.254+6230C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15633 AN: 151980 Hom.: 2156 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0628

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.103 AC: 15675 AN: 152100 Hom.: 2166 Cov.: 32 AF XY: 0.103 AC XY: 7657 AN XY: 74348

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.0418

Gnomad4 ASJ AF: 0.0153

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0622

Gnomad4 FIN AF: 0.0356

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.0843

Alfa AF: 0.0230 Hom.: 453

Bravo AF: 0.111

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.28
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs947425; hg19: chr1-119863356;