5-4029676-C-T

Variant names:

• chr5-4029676-C-T
• rs11748327

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 0.212 in 152,106 control chromosomes in the GnomAD database, including 3,994 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 0.21 (3994 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 24 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 (NFE) allele frequency at 95% confidence interval = 0.286 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: 0.212 AC: 32188 AN: 151988 Hom.: 3990 Cov.: 33

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.212 AC: 32200 AN: 152106 Hom.: 3994 Cov.: 33 AF XY: 0.208 AC XY: 15472 AN XY: 74340

African (AFR) AF: 0.0929 AC: 3857 AN: 41502

American (AMR) AF: 0.191 AC: 2915 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 824 AN: 3466

East Asian (EAS) AF: 0.145 AC: 753 AN: 5178

South Asian (SAS) AF: 0.228 AC: 1097 AN: 4816

European-Finnish (FIN) AF: 0.208 AC: 2200 AN: 10570

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19697 AN: 67984

Other (OTH) AF: 0.236 AC: 496 AN: 2102

Alfa AF: 0.255 Hom.: 10028

Bravo AF: 0.206

Asia WGS AF: 0.190 AC: 660 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.60
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11748327; hg19: chr5-4029789;