3-44241348-A-G

Variant names:

• chr3-44241348-A-G
• rs9846155

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 0.439 in 151,960 control chromosomes in the GnomAD database, including 16,288 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 0.44 (16288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 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: 0.439 AC: 66634 AN: 151842 Hom.: 16278 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.439 AC: 66667 AN: 151960 Hom.: 16288 Cov.: 32 AF XY: 0.448 AC XY: 33286 AN XY: 74240

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.442

Alfa AF: 0.335 Hom.: 1263

Bravo AF: 0.431

Asia WGS AF: 0.713 AC: 2480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9846155; hg19: chr3-44282840;