rs10500409

chr16-58966183-A-G

Variant summary

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

The ENST00000657379.1(ENSG00000245768):n.651-97999A>G 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 0.0421 in 152,262 control chromosomes in the GnomAD database, including 316 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 0.042 (316 hom., cov: 33)
• Consequence: ENST00000657379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657379.1	n.651-97999A>G		intron_variant, non_coding_transcript_variant
	ENST00000500117.1	n.680-97999A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0420 AC: 6395 AN: 152144 Hom.: 314 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0308

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00791

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0421 AC: 6413 AN: 152262 Hom.: 316 Cov.: 33 AF XY: 0.0405 AC XY: 3017 AN XY: 74448

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0233

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.0307

Gnomad4 FIN AF: 0.00141

Gnomad4 NFE AF: 0.00791

Gnomad4 OTH AF: 0.0436

Alfa AF: 0.0257 Hom.: 20

Bravo AF: 0.0471

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.6
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500409; hg19: chr16-59000087;