chr1-106889954-G-A

Variant names:

• chr1-106889954-G-A
• rs12726652

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 0.282 in 152,048 control chromosomes in the GnomAD database, including 7,105 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 0.28 (7105 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 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: 0.282 AC: 42790 AN: 151930 Hom.: 7086 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.282 AC: 42857 AN: 152048 Hom.: 7105 Cov.: 33 AF XY: 0.286 AC XY: 21228 AN XY: 74326

African (AFR) AF: 0.453 AC: 18799 AN: 41460

American (AMR) AF: 0.153 AC: 2339 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3470

East Asian (EAS) AF: 0.383 AC: 1976 AN: 5166

South Asian (SAS) AF: 0.285 AC: 1372 AN: 4822

European-Finnish (FIN) AF: 0.299 AC: 3158 AN: 10556

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14011 AN: 67976

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.221 Hom.: 15392

Bravo AF: 0.274

Asia WGS AF: 0.335 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs12726652; hg19: chr1-107432576;