rs1951923

Variant names:

• chr6-18352925-G-A
• rs1951923

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 0.312 in 152,010 control chromosomes in the GnomAD database, including 7,772 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 0.31 (7772 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.842

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 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: 0.312 AC: 47380 AN: 151892 Hom.: 7769 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.312 AC: 47395 AN: 152010 Hom.: 7772 Cov.: 32 AF XY: 0.311 AC XY: 23114 AN XY: 74264

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.326

Alfa AF: 0.340 Hom.: 2274

Bravo AF: 0.302

Asia WGS AF: 0.329 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1951923; hg19: chr6-18353156;