rs1551323

Positions:

• chr6-67115218-G-A
• chr6-67115218-G-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 0.112 in 152,108 control chromosomes in the GnomAD database, including 1,089 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 0.11 (1089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 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: 0.112 AC: 17081 AN: 151990 Hom.: 1090 Cov.: 32

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.112 AC: 17083 AN: 152108 Hom.: 1089 Cov.: 32 AF XY: 0.112 AC XY: 8308 AN XY: 74350

Gnomad4 AFR AF: 0.0733

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0345

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.134

Alfa AF: 0.0624 Hom.: 70

Bravo AF: 0.112

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1551323; hg19: chr6-67825111;