chr1-160113754-G-A

Variant names:

• chr1-160113754-G-A
• rs11265328

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 0.0858 in 152,256 control chromosomes in the GnomAD database, including 734 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 0.086 (734 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.111 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: 0.0858 AC: 13054 AN: 152138 Hom.: 732 Cov.: 33

Gnomad AFR AF: 0.0209

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0858 AC: 13064 AN: 152256 Hom.: 734 Cov.: 33 AF XY: 0.0869 AC XY: 6469 AN XY: 74436

African (AFR) AF: 0.0208 AC: 866 AN: 41562

American (AMR) AF: 0.115 AC: 1753 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3472

East Asian (EAS) AF: 0.0573 AC: 297 AN: 5180

South Asian (SAS) AF: 0.0684 AC: 330 AN: 4822

European-Finnish (FIN) AF: 0.136 AC: 1444 AN: 10598

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7725 AN: 68006

Other (OTH) AF: 0.0889 AC: 188 AN: 2114

Alfa AF: 0.0655 Hom.: 209

Bravo AF: 0.0798

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.73
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs11265328; hg19: chr1-160083544;