rs440317

Variant names:

• chr14-68863122-T-C
• rs440317

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 0.641 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.534 AC: 22128 AN: 41476

American (AMR) AF: 0.744 AC: 11369 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2227 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2898 AN: 5178

South Asian (SAS) AF: 0.693 AC: 3346 AN: 4830

European-Finnish (FIN) AF: 0.655 AC: 6917 AN: 10568

Middle Eastern (MID) AF: 0.634 AC: 184 AN: 290

European-Non Finnish (NFE) AF: 0.684 AC: 46485 AN: 67972

Other (OTH) AF: 0.647 AC: 1365 AN: 2110

Alfa AF: 0.664 Hom.: 8387

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs440317; hg19: chr14-69329839;