1-236296485-T-G

Variant names:

• chr1-236296485-T-G
• rs10924993

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.264 AC: 10934 AN: 41440

American (AMR) AF: 0.318 AC: 4852 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1596 AN: 3470

East Asian (EAS) AF: 0.0465 AC: 241 AN: 5186

South Asian (SAS) AF: 0.341 AC: 1640 AN: 4810

European-Finnish (FIN) AF: 0.408 AC: 4301 AN: 10534

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30694 AN: 67972

Other (OTH) AF: 0.374 AC: 787 AN: 2106

Alfa AF: 0.396 Hom.: 5588

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10924993; hg19: chr1-236459785;