chr1-171424687-G-C

Variant names:

• chr1-171424687-G-C
• rs17644596

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 0.0996 in 152,132 control chromosomes in the GnomAD database, including 1,063 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 0.10 (1063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.311 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: 0.0997 AC: 15163 AN: 152014 Hom.: 1061 Cov.: 32

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.0977

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

GnomAD4 genome AF: 0.0996 AC: 15157 AN: 152132 Hom.: 1063 Cov.: 32 AF XY: 0.103 AC XY: 7657 AN XY: 74360

Gnomad4 AFR AF: 0.0232

Gnomad4 AMR AF: 0.0862

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.00483

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.0962

Alfa AF: 0.0633 Hom.: 91

Bravo AF: 0.0867

Asia WGS AF: 0.138 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17644596; hg19: chr1-171393826;