rs717293

chr16-63524616-C-T

Variant summary

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

The ENST00000568932.5(ENSG00000260658):n.434+6609G>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 0.581 in 151,954 control chromosomes in the GnomAD database, including 27,418 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 0.58 (27418 hom., cov: 32)
• Consequence: ENST00000568932.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371308	XR_001752232.2	n.434+6609G>A		intron_variant, non_coding_transcript_variant
LOC105371308	XR_007065220.1	n.434+6609G>A		intron_variant, non_coding_transcript_variant
LOC105371308	XR_007065221.1	n.434+6609G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000568932.5	n.434+6609G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000655786.2	n.435-2838G>A		intron_variant, non_coding_transcript_variant
	ENST00000665929.1	n.434+6609G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88232 AN: 151836 Hom.: 27376 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.581 AC: 88312 AN: 151954 Hom.: 27418 Cov.: 32 AF XY: 0.569 AC XY: 42227 AN XY: 74256

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.621

Alfa AF: 0.527 Hom.: 28138

Bravo AF: 0.602

Asia WGS AF: 0.579 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.2
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs717293; hg19: chr16-63558520;