rs1418968

Variant names:

• chr6-18772867-G-A
• rs1418968

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 0.171 in 152,030 control chromosomes in the GnomAD database, including 3,371 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 0.17 (3371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -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 = 0.354 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: 0.171 AC: 25934 AN: 151912 Hom.: 3368 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.171 AC: 25972 AN: 152030 Hom.: 3371 Cov.: 32 AF XY: 0.170 AC XY: 12656 AN XY: 74348

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.0813

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0913

Gnomad4 NFE AF: 0.0792

Gnomad4 OTH AF: 0.167

Alfa AF: 0.0969 Hom.: 1206

Bravo AF: 0.185

Asia WGS AF: 0.148 AC: 514 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	2.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1418968; hg19: chr6-18773098;