rs1862751

Positions:

• chr16-63593979-T-A
• chr16-63593979-T-C
• chr16-63593979-T-G

Variant summary

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

The ENST00000568932.5(ENSG00000260658):​n.354+23714A>T 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 0.766 in 151,712 control chromosomes in the GnomAD database, including 45,056 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 0.77 (45056 hom., cov: 28)
• Consequence: ENST00000568932.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371308	XR_001752232.2	n.354+23714A>T		intron_variant, non_coding_transcript_variant
LOC105371308	XR_007065220.1	n.354+23714A>T		intron_variant, non_coding_transcript_variant
LOC105371308	XR_007065221.1	n.354+23714A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000568932.5	n.354+23714A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116055 AN: 151594 Hom.: 45009 Cov.: 28

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.766 AC: 116165 AN: 151712 Hom.: 45056 Cov.: 28 AF XY: 0.773 AC XY: 57271 AN XY: 74108

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.721

Alfa AF: 0.543 Hom.: 979

Bravo AF: 0.774

Asia WGS AF: 0.944 AC: 3278 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.94
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1862751; hg19: chr16-63627883;