rs1316604

Variant names:

• chr11-48258244-G-A
• rs1316604

Your query was ambiguous. Multiple possible variants found:

• chr11-48258244-G-A
• chr11-48258244-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 0.177 in 151,908 control chromosomes in the GnomAD database, including 2,768 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 0.18 (2768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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: 0.177 AC: 26942 AN: 151790 Hom.: 2766 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.177 AC: 26953 AN: 151908 Hom.: 2768 Cov.: 32 AF XY: 0.179 AC XY: 13269 AN XY: 74250

African (AFR) AF: 0.274 AC: 11358 AN: 41398

American (AMR) AF: 0.134 AC: 2035 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3470

East Asian (EAS) AF: 0.165 AC: 849 AN: 5156

South Asian (SAS) AF: 0.135 AC: 652 AN: 4812

European-Finnish (FIN) AF: 0.174 AC: 1841 AN: 10566

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.139 AC: 9415 AN: 67964

Other (OTH) AF: 0.136 AC: 286 AN: 2108

Alfa AF: 0.141 Hom.: 1109

Bravo AF: 0.178

Asia WGS AF: 0.131 AC: 453 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.32
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1316604; hg19: chr11-48279796;