1-96648359-T-G

Position:

• chr1-96648359-T-G

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 0.263 in 152,074 control chromosomes in the GnomAD database, including 6,553 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 0.26 (6553 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40025 AN: 151956 Hom.: 6539 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.263 AC: 40066 AN: 152074 Hom.: 6553 Cov.: 32 AF XY: 0.261 AC XY: 19397 AN XY: 74326

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.245

Alfa AF: 0.201 Hom.: 3038

Bravo AF: 0.270

Asia WGS AF: 0.210 AC: 731 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12071951; hg19: chr1-97113915; COSMIC: COSV59976173;