1-196875463-A-G

Variant summary

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

The ENST00000649395.1(ENSG00000285986):n.427-9143A>G 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 0.379 in 150,948 control chromosomes in the GnomAD database, including 13,098 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 0.38 (13098 hom., cov: 31)
• Consequence: ENST00000649395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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
	ENST00000649395.1	n.427-9143A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57218 AN: 150834 Hom.: 13087 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.379 AC: 57260 AN: 150948 Hom.: 13098 Cov.: 31 AF XY: 0.375 AC XY: 27624 AN XY: 73750

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.391

Alfa AF: 0.302 Hom.: 9496

Bravo AF: 0.394

Asia WGS AF: 0.281 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.7
Dann	Benign	0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6428370; hg19: chr1-196844593;