1-152577542-T-G

Variant names:

• chr1-152577542-T-G
• rs4085613

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 0.59 in 151,810 control chromosomes in the GnomAD database, including 27,005 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 0.59 (27005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 57 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89461 AN: 151694 Hom.: 26995 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.590 AC: 89502 AN: 151810 Hom.: 27005 Cov.: 32 AF XY: 0.594 AC XY: 44038 AN XY: 74180

African (AFR) AF: 0.457 AC: 18942 AN: 41414

American (AMR) AF: 0.615 AC: 9265 AN: 15074

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2158 AN: 3466

East Asian (EAS) AF: 0.612 AC: 3173 AN: 5182

South Asian (SAS) AF: 0.633 AC: 3050 AN: 4820

European-Finnish (FIN) AF: 0.665 AC: 7013 AN: 10552

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.646 AC: 43945 AN: 67986

Other (OTH) AF: 0.590 AC: 1247 AN: 2112

Alfa AF: 0.623 Hom.: 95159

Bravo AF: 0.578

Asia WGS AF: 0.587 AC: 2044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.40
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs4085613; hg19: chr1-152550018;