rs1488318

Variant names:

• chr6-93973885-G-A
• rs1488318

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 0.466 in 152,032 control chromosomes in the GnomAD database, including 17,500 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 0.47 (17500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.65 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: 0.466 AC: 70747 AN: 151912 Hom.: 17477 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.466 AC: 70818 AN: 152032 Hom.: 17500 Cov.: 32 AF XY: 0.470 AC XY: 34908 AN XY: 74284

African (AFR) AF: 0.303 AC: 12547 AN: 41448

American (AMR) AF: 0.497 AC: 7601 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1523 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3259 AN: 5152

South Asian (SAS) AF: 0.669 AC: 3224 AN: 4820

European-Finnish (FIN) AF: 0.490 AC: 5180 AN: 10570

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.531 AC: 36100 AN: 67976

Other (OTH) AF: 0.452 AC: 954 AN: 2110

Alfa AF: 0.495 Hom.: 8142

Bravo AF: 0.451

Asia WGS AF: 0.627 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.20
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1488318; hg19: chr6-94683603;