1-236296485-T-G

Position:

• chr1-236296485-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 0.366 in 151,980 control chromosomes in the GnomAD database, including 11,006 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 0.37 (11006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

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 (NFE) allele frequency at 95% confidence interval = 0.447 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: 0.366 AC: 55620 AN: 151862 Hom.: 11005 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.366 AC: 55634 AN: 151980 Hom.: 11006 Cov.: 32 AF XY: 0.363 AC XY: 26937 AN XY: 74270

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.374

Alfa AF: 0.391 Hom.: 4872

Bravo AF: 0.349

Asia WGS AF: 0.182 AC: 637 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	0.27
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10924993; hg19: chr1-236459785;