rs10500410

Positions:

• chr16-59034921-A-C
• chr16-59034921-A-G
• chr16-59034921-A-T

Variant summary

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

The ENST00000657379.1(ENSG00000245768):​n.651-29261A>C 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 0.111 in 152,206 control chromosomes in the GnomAD database, including 2,060 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 0.11 (2060 hom., cov: 32)
• Consequence: ENST00000657379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

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 (AFR) allele frequency at 95% confidence interval = 0.298 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
	ENST00000657379.1	n.651-29261A>C		intron_variant, non_coding_transcript_variant
	ENST00000500117.1	n.680-29261A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16864 AN: 152088 Hom.: 2056 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0277

Gnomad OTH AF: 0.0960

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

GnomAD4 genome AF: 0.111 AC: 16892 AN: 152206 Hom.: 2060 Cov.: 32 AF XY: 0.108 AC XY: 8016 AN XY: 74442

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.0569

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.0134

Gnomad4 NFE AF: 0.0277

Gnomad4 OTH AF: 0.0959

Alfa AF: 0.0367 Hom.: 212

Bravo AF: 0.125

Asia WGS AF: 0.119 AC: 414 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	7.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500410; hg19: chr16-59068825;