rs41451149

chr4-4840609-G-Achr4-4840609-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.137 in 152,146 control chromosomes in the GnomAD database, including 1,480 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 0.14 (1480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20879 AN: 152028 Hom.: 1476 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00656

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.137 AC: 20889 AN: 152146 Hom.: 1480 Cov.: 33 AF XY: 0.135 AC XY: 10021 AN XY: 74368

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.00658

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.142

Alfa AF: 0.125 Hom.: 475

Bravo AF: 0.136

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.30
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41451149; hg19: chr4-4842336;