1-113348496-C-T

Variant names:

• chr1-113348496-C-T
• rs9308261

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 0.302 in 151,680 control chromosomes in the GnomAD database, including 8,312 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 0.30 (8312 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 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: 0.303 AC: 45865 AN: 151564 Hom.: 8308 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.302 AC: 45868 AN: 151680 Hom.: 8312 Cov.: 31 AF XY: 0.303 AC XY: 22480 AN XY: 74086

African (AFR) AF: 0.105 AC: 4317 AN: 41280

American (AMR) AF: 0.339 AC: 5154 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1292 AN: 3466

East Asian (EAS) AF: 0.138 AC: 712 AN: 5166

South Asian (SAS) AF: 0.447 AC: 2146 AN: 4798

European-Finnish (FIN) AF: 0.378 AC: 3974 AN: 10502

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27287 AN: 67944

Other (OTH) AF: 0.290 AC: 609 AN: 2100

Alfa AF: 0.337 Hom.: 10729

Bravo AF: 0.286

Asia WGS AF: 0.305 AC: 1064 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.19
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs9308261; hg19: chr1-113891118;