rs1551323

Variant names:

• chr6-67115218-G-A
• rs1551323

Your query was ambiguous. Multiple possible variants found:

• chr6-67115218-G-A
• chr6-67115218-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0733 AC: 3042 AN: 41500

American (AMR) AF: 0.104 AC: 1587 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3470

East Asian (EAS) AF: 0.0345 AC: 179 AN: 5182

South Asian (SAS) AF: 0.127 AC: 614 AN: 4822

European-Finnish (FIN) AF: 0.110 AC: 1165 AN: 10584

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9490 AN: 67990

Other (OTH) AF: 0.134 AC: 283 AN: 2110

Alfa AF: 0.0632 Hom.: 72

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
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs1551323; hg19: chr6-67825111;