rs1336439

Variant names:

• chr10-81072501-T-C
• rs1336439

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 0.434 in 151,948 control chromosomes in the GnomAD database, including 15,171 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 0.43 (15171 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 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: 0.434 AC: 65901 AN: 151830 Hom.: 15146 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.434 AC: 65966 AN: 151948 Hom.: 15171 Cov.: 31 AF XY: 0.435 AC XY: 32315 AN XY: 74250

African (AFR) AF: 0.599 AC: 24824 AN: 41432

American (AMR) AF: 0.371 AC: 5662 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3466

East Asian (EAS) AF: 0.363 AC: 1866 AN: 5144

South Asian (SAS) AF: 0.323 AC: 1553 AN: 4810

European-Finnish (FIN) AF: 0.403 AC: 4262 AN: 10564

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25147 AN: 67960

Other (OTH) AF: 0.426 AC: 898 AN: 2108

Alfa AF: 0.396 Hom.: 26193

Bravo AF: 0.441

Asia WGS AF: 0.326 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.61
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1336439; hg19: chr10-82832257;