rs7542235

Variant names:

• chr1-196854483-A-G
• rs7542235

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 151,302 control chromosomes in the GnomAD database, including 4,990 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 (4990 hom., cov: 31)
• Consequence: LOC100996886 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 32 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100996886		n.196854483A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285986	ENST00000649395.1	n.59-3121A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34764 AN: 151186 Hom.: 4994 Cov.: 31

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0546

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.341

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: 34776 AN: 151302 Hom.: 4990 Cov.: 31 AF XY: 0.229 AC XY: 16962 AN XY: 73920

African (AFR) AF: 0.341 AC: 13973 AN: 40958

American (AMR) AF: 0.170 AC: 2580 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3466

East Asian (EAS) AF: 0.0545 AC: 281 AN: 5156

South Asian (SAS) AF: 0.324 AC: 1559 AN: 4812

European-Finnish (FIN) AF: 0.132 AC: 1390 AN: 10516

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.196 AC: 13319 AN: 67900

Other (OTH) AF: 0.253 AC: 531 AN: 2102

Alfa AF: 0.194 Hom.: 6315

Bravo AF: 0.233

Asia WGS AF: 0.203 AC: 707 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.15
PhyloP100		-0.41
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: rs7542235; hg19: chr1-196823613;