rs1016111

Variant names:

• chr6-14013467-C-G
• rs1016111

Your query was ambiguous. Multiple possible variants found:

• chr6-14013467-C-G
• chr6-14013467-C-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 0.333 in 150,932 control chromosomes in the GnomAD database, including 8,702 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 0.33 (8702 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 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: 0.333 AC: 50200 AN: 150814 Hom.: 8706 Cov.: 30

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.333 AC: 50231 AN: 150932 Hom.: 8702 Cov.: 30 AF XY: 0.334 AC XY: 24606 AN XY: 73676

African (AFR) AF: 0.371 AC: 15175 AN: 40924

American (AMR) AF: 0.353 AC: 5363 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 719 AN: 3464

East Asian (EAS) AF: 0.421 AC: 2164 AN: 5144

South Asian (SAS) AF: 0.469 AC: 2232 AN: 4760

European-Finnish (FIN) AF: 0.206 AC: 2142 AN: 10378

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.316 AC: 21447 AN: 67792

Other (OTH) AF: 0.295 AC: 615 AN: 2088

Alfa AF: 0.166 Hom.: 327

Bravo AF: 0.341

Asia WGS AF: 0.434 AC: 1507 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.60
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1016111; hg19: chr6-14013698;