1-168619944-T-G

Variant names:

• chr1-168619944-T-G
• rs2419117

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 0.438 in 152,076 control chromosomes in the GnomAD database, including 15,091 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 0.44 (15091 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 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: 0.438 AC: 66558 AN: 151958 Hom.: 15065 Cov.: 33

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.438 AC: 66613 AN: 152076 Hom.: 15091 Cov.: 33 AF XY: 0.446 AC XY: 33169 AN XY: 74350

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.404

Alfa AF: 0.388 Hom.: 5989

Bravo AF: 0.440

Asia WGS AF: 0.553 AC: 1924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2419117; hg19: chr1-168589182;