1-181847374-T-C

Variant names:

• chr1-181847374-T-C
• rs695072

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 0.337 in 152,024 control chromosomes in the GnomAD database, including 8,870 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 0.34 (8870 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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: 0.337 AC: 51134 AN: 151906 Hom.: 8861 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.337 AC: 51163 AN: 152024 Hom.: 8870 Cov.: 31 AF XY: 0.333 AC XY: 24759 AN XY: 74300

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.0876

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.368

Alfa AF: 0.360 Hom.: 20885

Bravo AF: 0.329

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs695072; hg19: chr1-181816509;