chr6-1318476-A-G

Variant names:

• chr6-1318476-A-G
• rs951318

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 0.0947 in 152,220 control chromosomes in the GnomAD database, including 907 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 0.095 (907 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.126 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: 0.0947 AC: 14407 AN: 152100 Hom.: 906 Cov.: 33

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0887

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0947 AC: 14409 AN: 152220 Hom.: 907 Cov.: 33 AF XY: 0.0955 AC XY: 7109 AN XY: 74408

African (AFR) AF: 0.0285 AC: 1186 AN: 41558

American (AMR) AF: 0.129 AC: 1970 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0836 AC: 290 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.0888 AC: 428 AN: 4822

European-Finnish (FIN) AF: 0.140 AC: 1486 AN: 10578

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8743 AN: 67998

Other (OTH) AF: 0.106 AC: 223 AN: 2108

Alfa AF: 0.117 Hom.: 638

Bravo AF: 0.0909

Asia WGS AF: 0.0360 AC: 124 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	6.5
DANN	Benign	0.59
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs951318; hg19: chr6-1318711;