chr1-175193669-G-T

Variant names:

• chr1-175193669-G-T
• rs3753555

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.488

Alfa AF: 0.536 Hom.: 34354

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3753555; hg19: chr1-175162805;