rs875975

Variant names:

• chr1-22249447-C-G
• rs875975

Your query was ambiguous. Multiple possible variants found:

• chr1-22249447-C-G
• chr1-22249447-C-T

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 0.193 in 152,162 control chromosomes in the GnomAD database, including 3,227 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 0.19 (3227 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 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: 0.193 AC: 29354 AN: 152044 Hom.: 3226 Cov.: 33

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.193 AC: 29359 AN: 152162 Hom.: 3227 Cov.: 33 AF XY: 0.196 AC XY: 14562 AN XY: 74380

Gnomad4 AFR AF: 0.0845

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.200

Alfa AF: 0.214 Hom.: 466

Bravo AF: 0.180

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs875975; hg19: chr1-22575940;