chr4-129333779-T-C

Variant names:

• chr4-129333779-T-C
• rs10518547

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 0.0533 in 152,208 control chromosomes in the GnomAD database, including 615 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 0.053 (615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• 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 = 0.161 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: 0.0533 AC: 8099 AN: 152090 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0305

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.00985

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00450

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0533 AC: 8119 AN: 152208 Hom.: 615 Cov.: 32 AF XY: 0.0536 AC XY: 3992 AN XY: 74426

African (AFR) AF: 0.164 AC: 6810 AN: 41510

American (AMR) AF: 0.0304 AC: 465 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3470

East Asian (EAS) AF: 0.00987 AC: 51 AN: 5168

South Asian (SAS) AF: 0.0635 AC: 306 AN: 4818

European-Finnish (FIN) AF: 0.00339 AC: 36 AN: 10616

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

European-Non Finnish (NFE) AF: 0.00448 AC: 305 AN: 68024

Other (OTH) AF: 0.0444 AC: 94 AN: 2116

Alfa AF: 0.0403 Hom.: 70

Bravo AF: 0.0599

Asia WGS AF: 0.0550 AC: 192 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	4.5
DANN	Benign	0.81
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10518547; hg19: chr4-130254934;