rs7519758

chr1-196856157-C-T

Variant summary

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

The ENST00000649395.1(ENSG00000285986):n.59-1447C>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 0.23 in 151,214 control chromosomes in the GnomAD database, including 4,995 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 0.23 (4995 hom., cov: 32)
• Consequence: ENST00000649395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 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.59-1447C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34779 AN: 151100 Hom.: 5000 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0651

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.230 AC: 34785 AN: 151214 Hom.: 4995 Cov.: 32 AF XY: 0.229 AC XY: 16933 AN XY: 73846

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.0650

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.252

Alfa AF: 0.208 Hom.: 520

Bravo AF: 0.234

Asia WGS AF: 0.206 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.2
Dann	Benign	0.61

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: rs7519758; hg19: chr1-196825287;