rs1901198

Variant names:

• chr7-129069735-A-G
• rs1901198

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 0.486 in 151,996 control chromosomes in the GnomAD database, including 18,213 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 0.49 (18213 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.52 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: 0.486 AC: 73805 AN: 151878 Hom.: 18201 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.486 AC: 73856 AN: 151996 Hom.: 18213 Cov.: 31 AF XY: 0.485 AC XY: 36045 AN XY: 74294

African (AFR) AF: 0.430 AC: 17824 AN: 41432

American (AMR) AF: 0.395 AC: 6034 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2162 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2346 AN: 5164

South Asian (SAS) AF: 0.538 AC: 2592 AN: 4822

European-Finnish (FIN) AF: 0.549 AC: 5810 AN: 10574

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.521 AC: 35403 AN: 67968

Other (OTH) AF: 0.482 AC: 1014 AN: 2104

Alfa AF: 0.510 Hom.: 19298

Bravo AF: 0.470

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.65
DANN	Benign	0.64
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs1901198; hg19: chr7-128709789;