1-96479241-A-C

Position:

• chr1-96479241-A-C

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 0.55 in 151,910 control chromosomes in the GnomAD database, including 23,633 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 0.55 (23633 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83506 AN: 151794 Hom.: 23632 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.550 AC: 83534 AN: 151910 Hom.: 23633 Cov.: 31 AF XY: 0.550 AC XY: 40790 AN XY: 74214

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.541

Alfa AF: 0.584 Hom.: 33128

Bravo AF: 0.546

Asia WGS AF: 0.705 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555543; hg19: chr1-96944797;