3-38844922-C-A

Variant names:

• chr3-38844922-C-A
• rs3923518

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 0.231 in 152,004 control chromosomes in the GnomAD database, including 4,166 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 0.23 (4166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 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: 0.231 AC: 35059 AN: 151886 Hom.: 4169 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.231 AC: 35069 AN: 152004 Hom.: 4166 Cov.: 32 AF XY: 0.230 AC XY: 17079 AN XY: 74326

African (AFR) AF: 0.211 AC: 8725 AN: 41448

American (AMR) AF: 0.249 AC: 3803 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3472

East Asian (EAS) AF: 0.130 AC: 672 AN: 5180

South Asian (SAS) AF: 0.166 AC: 800 AN: 4818

European-Finnish (FIN) AF: 0.243 AC: 2558 AN: 10542

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17068 AN: 67946

Other (OTH) AF: 0.220 AC: 465 AN: 2114

Alfa AF: 0.242 Hom.: 18367

Bravo AF: 0.234

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs3923518; hg19: chr3-38886413;