chr13-20274178-C-T

Variant names:

• chr13-20274178-C-T
• rs7992230

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 0.323 in 151,908 control chromosomes in the GnomAD database, including 9,146 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 0.32 (9146 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.409 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: 0.323 AC: 48961 AN: 151790 Hom.: 9136 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.323 AC: 49006 AN: 151908 Hom.: 9146 Cov.: 32 AF XY: 0.325 AC XY: 24127 AN XY: 74280

African (AFR) AF: 0.142 AC: 5864 AN: 41422

American (AMR) AF: 0.288 AC: 4398 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3466

East Asian (EAS) AF: 0.377 AC: 1953 AN: 5176

South Asian (SAS) AF: 0.401 AC: 1928 AN: 4808

European-Finnish (FIN) AF: 0.430 AC: 4530 AN: 10536

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.413 AC: 28080 AN: 67926

Other (OTH) AF: 0.331 AC: 700 AN: 2112

Alfa AF: 0.378 Hom.: 44582

Bravo AF: 0.300

Asia WGS AF: 0.452 AC: 1571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7992230; hg19: chr13-20848317;