chr1-202975018-G-A

Variant names:

• chr1-202975018-G-A
• rs7554506

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 0.305 in 152,100 control chromosomes in the GnomAD database, including 7,418 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 0.30 (7418 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 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: 0.305 AC: 46320 AN: 151982 Hom.: 7419 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.305 AC: 46331 AN: 152100 Hom.: 7418 Cov.: 32 AF XY: 0.301 AC XY: 22377 AN XY: 74360

African (AFR) AF: 0.268 AC: 11115 AN: 41474

American (AMR) AF: 0.290 AC: 4440 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1490 AN: 3470

East Asian (EAS) AF: 0.0589 AC: 305 AN: 5182

South Asian (SAS) AF: 0.265 AC: 1280 AN: 4822

European-Finnish (FIN) AF: 0.264 AC: 2797 AN: 10576

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.346 AC: 23511 AN: 67986

Other (OTH) AF: 0.316 AC: 664 AN: 2102

Alfa AF: 0.176 Hom.: 347

Bravo AF: 0.304

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.8
DANN	Benign	0.68
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7554506; hg19: chr1-202944146;