13-44902673-C-T

Variant names:

• chr13-44902673-C-T
• rs6561194

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 0.189 in 152,110 control chromosomes in the GnomAD database, including 2,973 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 0.19 (2973 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 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: 0.189 AC: 28774 AN: 151992 Hom.: 2970 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.189 AC: 28784 AN: 152110 Hom.: 2973 Cov.: 32 AF XY: 0.190 AC XY: 14091 AN XY: 74348

African (AFR) AF: 0.131 AC: 5431 AN: 41520

American (AMR) AF: 0.158 AC: 2412 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3468

East Asian (EAS) AF: 0.0348 AC: 180 AN: 5178

South Asian (SAS) AF: 0.115 AC: 554 AN: 4814

European-Finnish (FIN) AF: 0.279 AC: 2947 AN: 10562

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15683 AN: 67972

Other (OTH) AF: 0.196 AC: 413 AN: 2106

Alfa AF: 0.211 Hom.: 7879

Bravo AF: 0.180

Asia WGS AF: 0.0760 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.42
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6561194; hg19: chr13-45476808;