rs6567160

Variant names:

• chr18-60161902-T-C
• rs6567160

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.211 in 152,146 control chromosomes in the GnomAD database, including 3,546 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 0.21 (3546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 186 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.336 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: 0.211 AC: 32040 AN: 152028 Hom.: 3542 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.211 AC: 32058 AN: 152146 Hom.: 3546 Cov.: 32 AF XY: 0.209 AC XY: 15520 AN XY: 74380

African (AFR) AF: 0.189 AC: 7844 AN: 41510

American (AMR) AF: 0.150 AC: 2296 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 709 AN: 3468

East Asian (EAS) AF: 0.181 AC: 941 AN: 5190

South Asian (SAS) AF: 0.350 AC: 1684 AN: 4816

European-Finnish (FIN) AF: 0.171 AC: 1810 AN: 10588

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15957 AN: 67988

Other (OTH) AF: 0.213 AC: 450 AN: 2112

Alfa AF: 0.223 Hom.: 9705

Bravo AF: 0.206

Asia WGS AF: 0.221 AC: 769 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	17
DANN	Benign	0.81
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6567160; hg19: chr18-57829135;