chr1-175193669-G-T

Variant names:

• chr1-175193669-G-T
• rs3753555

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 0.489 in 151,924 control chromosomes in the GnomAD database, including 18,677 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 0.49 (18677 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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: 0.489 AC: 74229 AN: 151808 Hom.: 18684 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.489 AC: 74237 AN: 151924 Hom.: 18677 Cov.: 31 AF XY: 0.489 AC XY: 36328 AN XY: 74234

African (AFR) AF: 0.382 AC: 15839 AN: 41434

American (AMR) AF: 0.407 AC: 6213 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1493 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2188 AN: 5152

South Asian (SAS) AF: 0.528 AC: 2547 AN: 4820

European-Finnish (FIN) AF: 0.601 AC: 6334 AN: 10536

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.560 AC: 38041 AN: 67926

Other (OTH) AF: 0.488 AC: 1029 AN: 2108

Alfa AF: 0.527 Hom.: 79446

Bravo AF: 0.464

Asia WGS AF: 0.466 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.70
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs3753555; hg19: chr1-175162805;