rs39968

Positions:

• chr5-14570623-A-G

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 0.71 in 152,176 control chromosomes in the GnomAD database, including 38,718 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 0.71 (38718 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

ACMG classification

Verdict is Benign. Variant got -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 = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107900 AN: 152058 Hom.: 38673 Cov.: 33

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.710 AC: 108003 AN: 152176 Hom.: 38718 Cov.: 33 AF XY: 0.706 AC XY: 52522 AN XY: 74398

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.711

Alfa AF: 0.686 Hom.: 48426

Bravo AF: 0.717

Asia WGS AF: 0.625 AC: 2176 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	0.16
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs39968; hg19: chr5-14570732;