chr16-64475513-G-A

Variant names:

• chr16-64475513-G-A
• rs1862791
• ENST00000564046.1:n.117-176G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000564046.1(ENSG00000259846):​n.117-176G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0441 in 152,046 control chromosomes in the GnomAD database, including 440 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 0.044 (440 hom., cov: 32)
• Consequence: ENSG00000259846 ENST00000564046.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 1 publications found

Genes affected

ENSG00000259846 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371310	XR_001752233.1	n.225-176G>A		intron_variant	Intron 2 of 3
LOC105371310	XR_001752234.1	n.207-176G>A		intron_variant	Intron 2 of 3
LOC105371310	XR_001752236.1	n.291-176G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259846	ENST00000564046.1	n.117-176G>A		intron_variant	Intron 1 of 4	4
ENSG00000259846	ENST00000808892.1	n.180-176G>A		intron_variant	Intron 1 of 4
ENSG00000259846	ENST00000808893.1	n.166-176G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0440 AC: 6691 AN: 151936 Hom.: 440 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0184

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0999

Gnomad FIN AF: 0.000473

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.00382

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0441 AC: 6698 AN: 152046 Hom.: 440 Cov.: 32 AF XY: 0.0447 AC XY: 3320 AN XY: 74310

African (AFR) AF: 0.134 AC: 5537 AN: 41460

American (AMR) AF: 0.0183 AC: 279 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3472

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5158

South Asian (SAS) AF: 0.0996 AC: 480 AN: 4820

European-Finnish (FIN) AF: 0.000473 AC: 5 AN: 10566

Middle Eastern (MID) AF: 0.0240 AC: 7 AN: 292

European-Non Finnish (NFE) AF: 0.00382 AC: 260 AN: 67992

Other (OTH) AF: 0.0379 AC: 80 AN: 2110

Alfa AF: 0.0236 Hom.: 63

Bravo AF: 0.0467

Asia WGS AF: 0.0540 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.38
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1862791; hg19: chr16-64509416;