13-44334605-T-C

Variant names:

• chr13-44334605-T-C
• rs9567416

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 0.274 in 152,096 control chromosomes in the GnomAD database, including 5,737 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 0.27 (5737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 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: 0.274 AC: 41680 AN: 151978 Hom.: 5736 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.274 AC: 41699 AN: 152096 Hom.: 5737 Cov.: 32 AF XY: 0.276 AC XY: 20549 AN XY: 74342

African (AFR) AF: 0.309 AC: 12812 AN: 41486

American (AMR) AF: 0.255 AC: 3896 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3470

East Asian (EAS) AF: 0.321 AC: 1661 AN: 5178

South Asian (SAS) AF: 0.336 AC: 1619 AN: 4814

European-Finnish (FIN) AF: 0.261 AC: 2762 AN: 10566

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17221 AN: 67992

Other (OTH) AF: 0.263 AC: 554 AN: 2106

Alfa AF: 0.265 Hom.: 2183

Bravo AF: 0.273

Asia WGS AF: 0.317 AC: 1102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.60
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs9567416; hg19: chr13-44908741;