chr1-156892401-T-C

Variant names:

• chr1-156892401-T-C
• rs4661069

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 0.849 in 151,904 control chromosomes in the GnomAD database, including 55,015 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 0.85 (55015 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.88 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: 0.849 AC: 128928 AN: 151786 Hom.: 54970 Cov.: 28

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.849 AC: 129024 AN: 151904 Hom.: 55015 Cov.: 28 AF XY: 0.845 AC XY: 62713 AN XY: 74236

African (AFR) AF: 0.819 AC: 33913 AN: 41410

American (AMR) AF: 0.839 AC: 12823 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3037 AN: 3468

East Asian (EAS) AF: 0.662 AC: 3386 AN: 5116

South Asian (SAS) AF: 0.806 AC: 3854 AN: 4780

European-Finnish (FIN) AF: 0.848 AC: 8967 AN: 10578

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60221 AN: 67962

Other (OTH) AF: 0.855 AC: 1798 AN: 2104

Alfa AF: 0.858 Hom.: 2776

Bravo AF: 0.848

Asia WGS AF: 0.728 AC: 2536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs4661069; hg19: chr1-156862193;