16-76276723-C-T

Position:

• chr16-76276723-C-T

Variant summary

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

The ENST00000657635.1(ENSG00000286841):​n.241+340G>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 0.383 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: ENST00000657635.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657635.1	n.241+340G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.401

Alfa AF: 0.368 Hom.: 8331

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6564312; hg19: chr16-76310621;