chr14-47929318-T-C

Variant names:

• chr14-47929318-T-C
• rs2770409

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 0.358 in 151,970 control chromosomes in the GnomAD database, including 10,423 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 0.36 (10423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.446 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: 0.358 AC: 54339 AN: 151852 Hom.: 10414 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.358 AC: 54372 AN: 151970 Hom.: 10423 Cov.: 32 AF XY: 0.362 AC XY: 26899 AN XY: 74258

African (AFR) AF: 0.237 AC: 9823 AN: 41474

American (AMR) AF: 0.429 AC: 6552 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1369 AN: 3472

East Asian (EAS) AF: 0.193 AC: 997 AN: 5174

South Asian (SAS) AF: 0.462 AC: 2221 AN: 4812

European-Finnish (FIN) AF: 0.477 AC: 5008 AN: 10502

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.401 AC: 27243 AN: 67946

Other (OTH) AF: 0.340 AC: 719 AN: 2114

Alfa AF: 0.399 Hom.: 5436

Bravo AF: 0.346

Asia WGS AF: 0.290 AC: 1004 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.48
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2770409; hg19: chr14-48398521;