chr14-40575322-T-C

Variant names:

• chr14-40575322-T-C
• rs2415621

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 0.275 in 151,820 control chromosomes in the GnomAD database, including 5,914 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 0.28 (5914 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 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: 0.275 AC: 41715 AN: 151702 Hom.: 5910 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.275 AC: 41751 AN: 151820 Hom.: 5914 Cov.: 32 AF XY: 0.270 AC XY: 19993 AN XY: 74168

African (AFR) AF: 0.329 AC: 13628 AN: 41450

American (AMR) AF: 0.220 AC: 3343 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1082 AN: 5134

South Asian (SAS) AF: 0.266 AC: 1284 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2347 AN: 10584

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18184 AN: 67878

Other (OTH) AF: 0.248 AC: 525 AN: 2114

Alfa AF: 0.250 Hom.: 2528

Bravo AF: 0.276

Asia WGS AF: 0.232 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2415621; hg19: chr14-41044527;