1-153349108-G-T

Variant names:

• chr1-153349108-G-T
• rs3014864

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 0.83 in 152,194 control chromosomes in the GnomAD database, including 52,610 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 0.83 (52610 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 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: 0.830 AC: 126239 AN: 152076 Hom.: 52583 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.830 AC: 126319 AN: 152194 Hom.: 52610 Cov.: 32 AF XY: 0.833 AC XY: 61977 AN XY: 74398

African (AFR) AF: 0.757 AC: 31432 AN: 41532

American (AMR) AF: 0.849 AC: 12982 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2928 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4538 AN: 5170

South Asian (SAS) AF: 0.838 AC: 4037 AN: 4820

European-Finnish (FIN) AF: 0.891 AC: 9447 AN: 10606

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58144 AN: 67984

Other (OTH) AF: 0.837 AC: 1768 AN: 2112

Alfa AF: 0.847 Hom.: 27527

Bravo AF: 0.822

Asia WGS AF: 0.846 AC: 2944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		0.29
PromoterAI		0.050	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3014864; hg19: chr1-153321584;