rs13150247

Variant names:

• chr4-99720811-T-C
• rs13150247

Your query was ambiguous. Multiple possible variants found:

• chr4-99720811-T-C
• chr4-99720811-T-G

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 0.103 in 152,138 control chromosomes in the GnomAD database, including 1,275 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 0.10 (1275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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: 0.103 AC: 15645 AN: 152020 Hom.: 1262 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.0450

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0883

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

GnomAD4 genome AF: 0.103 AC: 15693 AN: 152138 Hom.: 1275 Cov.: 32 AF XY: 0.102 AC XY: 7588 AN XY: 74394

African (AFR) AF: 0.203 AC: 8427 AN: 41466

American (AMR) AF: 0.141 AC: 2153 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3468

East Asian (EAS) AF: 0.192 AC: 991 AN: 5162

South Asian (SAS) AF: 0.0448 AC: 216 AN: 4822

European-Finnish (FIN) AF: 0.0223 AC: 237 AN: 10612

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0485 AC: 3296 AN: 68010

Other (OTH) AF: 0.0917 AC: 194 AN: 2116

Alfa AF: 0.0610 Hom.: 264

Bravo AF: 0.116

Asia WGS AF: 0.113 AC: 390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.79
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs13150247; hg19: chr4-100641968;