rs999460

Positions:

• chr14-36515306-C-T

Variant summary

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

The NR_161364.1(SFTA3):​n.89+4162G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,216 control chromosomes in the GnomAD database, including 6,047 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 0.25 (6047 hom., cov: 33)
• Consequence: SFTA3 NR_161364.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFTA3	NR_161364.1	n.89+4162G>A		intron_variant, non_coding_transcript_variant
SFTA3	NR_161365.1	n.89+4162G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634305.1	n.322+66469C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38116 AN: 152098 Hom.: 6047 Cov.: 33

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.250 AC: 38118 AN: 152216 Hom.: 6047 Cov.: 33 AF XY: 0.244 AC XY: 18177 AN XY: 74408

Gnomad4 AFR AF: 0.0822

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.0626

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.284

Alfa AF: 0.320 Hom.: 2509

Bravo AF: 0.237

Asia WGS AF: 0.124 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs999460; hg19: chr14-36984511;