rs440317

Variant names:

• chr14-68863122-T-C
• rs440317

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.641 in 152,080 control chromosomes in the GnomAD database, including 31,869 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 0.64 (31869 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.733 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: 0.642 AC: 97484 AN: 151962 Hom.: 31843 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.651

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.641 AC: 97542 AN: 152080 Hom.: 31869 Cov.: 32 AF XY: 0.642 AC XY: 47705 AN XY: 74326

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.647

Alfa AF: 0.667 Hom.: 8274

Bravo AF: 0.641

Asia WGS AF: 0.676 AC: 2347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.8
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs440317; hg19: chr14-69329839;