1-160108064-C-T

Variant names:

• chr1-160108064-C-T
• rs6688363

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 0.166 in 152,148 control chromosomes in the GnomAD database, including 2,409 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 0.17 (2409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.166 AC: 25277 AN: 152030 Hom.: 2401 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.166 AC: 25310 AN: 152148 Hom.: 2409 Cov.: 32 AF XY: 0.170 AC XY: 12622 AN XY: 74360

African (AFR) AF: 0.115 AC: 4755 AN: 41500

American (AMR) AF: 0.297 AC: 4538 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 630 AN: 3472

East Asian (EAS) AF: 0.324 AC: 1679 AN: 5180

South Asian (SAS) AF: 0.190 AC: 915 AN: 4820

European-Finnish (FIN) AF: 0.122 AC: 1296 AN: 10580

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10829 AN: 68014

Other (OTH) AF: 0.203 AC: 429 AN: 2110

Alfa AF: 0.171 Hom.: 6810

Bravo AF: 0.182

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.87
DANN	Benign	0.46
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs6688363; hg19: chr1-160077854;