rs198372

Variant names:

• chr1-11849457-G-A
• rs198372

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 0.129 in 152,204 control chromosomes in the GnomAD database, including 1,388 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 0.13 (1388 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 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: 0.129 AC: 19543 AN: 152086 Hom.: 1386 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.00846

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0631

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.129 AC: 19580 AN: 152204 Hom.: 1388 Cov.: 32 AF XY: 0.126 AC XY: 9390 AN XY: 74426

African (AFR) AF: 0.164 AC: 6823 AN: 41516

American (AMR) AF: 0.0912 AC: 1395 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3468

East Asian (EAS) AF: 0.00847 AC: 44 AN: 5192

South Asian (SAS) AF: 0.158 AC: 761 AN: 4822

European-Finnish (FIN) AF: 0.0631 AC: 670 AN: 10616

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9041 AN: 67982

Other (OTH) AF: 0.128 AC: 269 AN: 2108

Alfa AF: 0.132 Hom.: 4282

Bravo AF: 0.131

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.40
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs198372; hg19: chr1-11909514;