chr3-145418990-C-A

Variant names:

• chr3-145418990-C-A
• rs344985

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 0.087 in 151,760 control chromosomes in the GnomAD database, including 741 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 0.087 (741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 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: 0.0871 AC: 13211 AN: 151644 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.0221

Gnomad AMI AF: 0.0299

Gnomad AMR AF: 0.0852

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0870 AC: 13203 AN: 151760 Hom.: 741 Cov.: 32 AF XY: 0.0862 AC XY: 6390 AN XY: 74168

African (AFR) AF: 0.0221 AC: 919 AN: 41490

American (AMR) AF: 0.0852 AC: 1297 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 431 AN: 3458

East Asian (EAS) AF: 0.151 AC: 780 AN: 5178

South Asian (SAS) AF: 0.0986 AC: 474 AN: 4808

European-Finnish (FIN) AF: 0.0817 AC: 863 AN: 10568

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.120 AC: 8137 AN: 67746

Other (OTH) AF: 0.103 AC: 217 AN: 2102

Alfa AF: 0.0937 Hom.: 133

Bravo AF: 0.0834

Asia WGS AF: 0.132 AC: 459 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.67
DANN	Benign	0.53
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs344985; hg19: chr3-145136777;