1-175155900-C-T

Variant names:

• chr1-175155900-C-T
• rs6425323

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 0.387 in 152,018 control chromosomes in the GnomAD database, including 11,963 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 0.39 (11963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 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: 0.387 AC: 58761 AN: 151900 Hom.: 11960 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.387 AC: 58787 AN: 152018 Hom.: 11963 Cov.: 32 AF XY: 0.384 AC XY: 28547 AN XY: 74270

African (AFR) AF: 0.335 AC: 13899 AN: 41442

American (AMR) AF: 0.320 AC: 4894 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3470

East Asian (EAS) AF: 0.0970 AC: 502 AN: 5176

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4820

European-Finnish (FIN) AF: 0.501 AC: 5277 AN: 10542

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30850 AN: 67960

Other (OTH) AF: 0.373 AC: 788 AN: 2110

Alfa AF: 0.406 Hom.: 34090

Bravo AF: 0.368

Asia WGS AF: 0.194 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.14
DANN	Benign	0.34
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6425323; hg19: chr1-175125036;