3-45042436-T-C

Variant names:

• chr3-45042436-T-C
• rs10514712

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 0.173 in 152,192 control chromosomes in the GnomAD database, including 2,759 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 0.17 (2759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 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: 0.174 AC: 26393 AN: 152074 Hom.: 2753 Cov.: 32

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0997

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.173 AC: 26402 AN: 152192 Hom.: 2759 Cov.: 32 AF XY: 0.172 AC XY: 12781 AN XY: 74408

African (AFR) AF: 0.0669 AC: 2780 AN: 41548

American (AMR) AF: 0.257 AC: 3929 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3464

East Asian (EAS) AF: 0.100 AC: 519 AN: 5184

South Asian (SAS) AF: 0.198 AC: 956 AN: 4828

European-Finnish (FIN) AF: 0.180 AC: 1903 AN: 10596

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14749 AN: 67970

Other (OTH) AF: 0.210 AC: 445 AN: 2116

Alfa AF: 0.215 Hom.: 7476

Bravo AF: 0.175

Asia WGS AF: 0.137 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.7
DANN	Benign	0.75
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs10514712; hg19: chr3-45083928;