16-76276723-C-T

Variant names:

• chr16-76276723-C-T
• rs6564312
• ENST00000657635.1:n.241+340G>A

Variant summary

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

The ENST00000657635.1(ENSG00000286841):​n.241+340G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,026 control chromosomes in the GnomAD database, including 11,282 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 0.38 (11282 hom., cov: 32)
• Consequence: ENSG00000286841 ENST00000657635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 0 publications found

Genes affected

ENSG00000286841 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286841	ENST00000657635.1	n.241+340G>A		intron_variant	Intron 1 of 1
ENSG00000307481	ENST00000826518.1	n.304-19140C>T		intron_variant	Intron 3 of 3
ENSG00000286841	ENST00000826621.1	n.242+340G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58145 AN: 151908 Hom.: 11267 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.383 AC: 58204 AN: 152026 Hom.: 11282 Cov.: 32 AF XY: 0.387 AC XY: 28761 AN XY: 74308

African (AFR) AF: 0.358 AC: 14861 AN: 41466

American (AMR) AF: 0.475 AC: 7260 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1289 AN: 3466

East Asian (EAS) AF: 0.520 AC: 2689 AN: 5176

South Asian (SAS) AF: 0.486 AC: 2343 AN: 4822

European-Finnish (FIN) AF: 0.337 AC: 3555 AN: 10548

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25022 AN: 67962

Other (OTH) AF: 0.401 AC: 846 AN: 2108

Alfa AF: 0.376 Hom.: 26096

Bravo AF: 0.394

Asia WGS AF: 0.546 AC: 1896 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	7.8
DANN	Benign	0.30
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs6564312; hg19: chr16-76310621;