chr16-85930957-T-C

Position:

• chr16-85930957-T-C

Variant summary

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

The ENST00000646214.1(ENSG00000285163):​n.77+5897T>C 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 0.148 in 152,188 control chromosomes in the GnomAD database, including 1,772 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 0.15 (1772 hom., cov: 33)
• Consequence: ENST00000646214.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646214.1	n.77+5897T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22452 AN: 152070 Hom.: 1770 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.148 AC: 22467 AN: 152188 Hom.: 1772 Cov.: 33 AF XY: 0.148 AC XY: 10979 AN XY: 74410

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0649

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.130

Alfa AF: 0.143 Hom.: 815

Bravo AF: 0.149

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs366078; hg19: chr16-85964563;