3-180351784-T-C

Variant names:

• chr3-180351784-T-C
• rs1402229

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 0.255 in 152,068 control chromosomes in the GnomAD database, including 5,695 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 0.25 (5695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.443 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: 0.255 AC: 38720 AN: 151950 Hom.: 5691 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.255 AC: 38747 AN: 152068 Hom.: 5695 Cov.: 32 AF XY: 0.264 AC XY: 19593 AN XY: 74326

African (AFR) AF: 0.122 AC: 5053 AN: 41520

American (AMR) AF: 0.370 AC: 5646 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 841 AN: 3472

East Asian (EAS) AF: 0.383 AC: 1982 AN: 5172

South Asian (SAS) AF: 0.459 AC: 2208 AN: 4808

European-Finnish (FIN) AF: 0.337 AC: 3555 AN: 10562

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18599 AN: 67958

Other (OTH) AF: 0.271 AC: 573 AN: 2112

Alfa AF: 0.270 Hom.: 4423

Bravo AF: 0.249

Asia WGS AF: 0.407 AC: 1416 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	2.0
DANN	Benign	0.25
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1402229; hg19: chr3-180069572;