chr16-62547042-C-T

Variant names:

• chr16-62547042-C-T
• rs2911292
• ENST00000841257.1:n.103-22973C>T

Variant summary

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

The ENST00000841257.1(ENSG00000309454):​n.103-22973C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,594 control chromosomes in the GnomAD database, including 13,347 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 0.41 (13347 hom., cov: 32)
• Consequence: ENSG00000309454 ENST00000841257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440
• Publications: 1 publications found

Genes affected

ENSG00000309454 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 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
ENSG00000309454	ENST00000841257.1	n.103-22973C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62356 AN: 151478 Hom.: 13327 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.412 AC: 62425 AN: 151594 Hom.: 13347 Cov.: 32 AF XY: 0.412 AC XY: 30491 AN XY: 74056

African (AFR) AF: 0.535 AC: 22137 AN: 41360

American (AMR) AF: 0.270 AC: 4115 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1324 AN: 3464

East Asian (EAS) AF: 0.413 AC: 2098 AN: 5076

South Asian (SAS) AF: 0.373 AC: 1796 AN: 4818

European-Finnish (FIN) AF: 0.430 AC: 4538 AN: 10562

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.372 AC: 25195 AN: 67784

Other (OTH) AF: 0.384 AC: 807 AN: 2100

Alfa AF: 0.420 Hom.: 1941

Bravo AF: 0.401

Asia WGS AF: 0.430 AC: 1497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.5
DANN	Benign	0.50
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2911292; hg19: chr16-62580946;