rs198375

Variant names:

• chr1-11853700-T-C
• rs198375

Your query was ambiguous. Multiple possible variants found:

• chr1-11853700-T-C
• chr1-11853700-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.434 in 151,808 control chromosomes in the GnomAD database, including 15,212 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 0.43 (15212 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.434 AC: 65818 AN: 151690 Hom.: 15194 Cov.: 31

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.434 AC: 65871 AN: 151808 Hom.: 15212 Cov.: 31 AF XY: 0.431 AC XY: 31977 AN XY: 74172

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.420

Alfa AF: 0.397 Hom.: 12850

Bravo AF: 0.431

Asia WGS AF: 0.352 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs198375; hg19: chr1-11913757;