1-155154472-T-C

Variant names:

• chr1-155154472-T-C
• rs10908458

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 0.424 in 151,988 control chromosomes in the GnomAD database, including 14,350 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 0.42 (14350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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: 0.424 AC: 64352 AN: 151870 Hom.: 14344 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.424 AC: 64386 AN: 151988 Hom.: 14350 Cov.: 32 AF XY: 0.430 AC XY: 31949 AN XY: 74274

African (AFR) AF: 0.358 AC: 14843 AN: 41438

American (AMR) AF: 0.527 AC: 8042 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1267 AN: 3466

East Asian (EAS) AF: 0.820 AC: 4258 AN: 5192

South Asian (SAS) AF: 0.481 AC: 2314 AN: 4812

European-Finnish (FIN) AF: 0.462 AC: 4867 AN: 10526

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.404 AC: 27452 AN: 67974

Other (OTH) AF: 0.409 AC: 864 AN: 2110

Alfa AF: 0.423 Hom.: 4159

Bravo AF: 0.431

Asia WGS AF: 0.595 AC: 2068 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	0.77
DANN	Benign	0.17
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10908458; hg19: chr1-155126948;