rs7519758

Variant names:

• chr1-196856157-C-T
• rs7519758

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: LOC100996886 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 6 publications found

Genes affected

LOC100996886 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC100996886		n.196856157C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285986	ENST00000649395.1	n.59-1447C>T		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.341 AC: 13974 AN: 40948

American (AMR) AF: 0.170 AC: 2580 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3464

East Asian (EAS) AF: 0.0650 AC: 336 AN: 5166

South Asian (SAS) AF: 0.325 AC: 1562 AN: 4810

European-Finnish (FIN) AF: 0.131 AC: 1373 AN: 10488

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.196 AC: 13294 AN: 67874

Other (OTH) AF: 0.252 AC: 527 AN: 2090

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
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7519758; hg19: chr1-196825287;