rs1951923

Positions:

• chr6-18352925-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;