chr3-145753975-G-A

Variant names:

• chr3-145753975-G-A
• rs6770324

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 0.238 in 152,064 control chromosomes in the GnomAD database, including 4,606 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 0.24 (4606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 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: 0.239 AC: 36252 AN: 151946 Hom.: 4611 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.238 AC: 36252 AN: 152064 Hom.: 4606 Cov.: 32 AF XY: 0.239 AC XY: 17792 AN XY: 74350

African (AFR) AF: 0.168 AC: 6969 AN: 41508

American (AMR) AF: 0.204 AC: 3121 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3468

East Asian (EAS) AF: 0.155 AC: 799 AN: 5158

South Asian (SAS) AF: 0.177 AC: 856 AN: 4826

European-Finnish (FIN) AF: 0.319 AC: 3375 AN: 10576

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19035 AN: 67950

Other (OTH) AF: 0.248 AC: 523 AN: 2106

Alfa AF: 0.257 Hom.: 6654

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.2
DANN	Benign	0.66
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs6770324; hg19: chr3-145471762;