rs7552547

chr1-196867869-T-G

Variant summary

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

The ENST00000649395.1(ENSG00000285986):n.426+9465T>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 0.21 in 150,584 control chromosomes in the GnomAD database, including 5,359 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 0.21 (5359 hom., cov: 32)
• Consequence: ENST00000649395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 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.426+9465T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31634 AN: 150468 Hom.: 5353 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000970

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.210 AC: 31664 AN: 150584 Hom.: 5359 Cov.: 32 AF XY: 0.208 AC XY: 15306 AN XY: 73628

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.000972

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.209

Alfa AF: 0.181 Hom.: 604

Bravo AF: 0.221

Asia WGS AF: 0.0910 AC: 316 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	2.1
Dann	Benign	0.27

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: rs7552547; hg19: chr1-196836999;