rs947425

chr1-119320733-G-A

Variant summary

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

The ENST00000655614.1(ENSG00000227712):n.254+6230C>T variant causes a intron, non coding transcript 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: ENST00000655614.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655614.1	n.254+6230C>T		intron_variant, non_coding_transcript_variant

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;