rs16867579

Positions:

• chr8-101363039-A-C

Variant summary

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

The ENST00000419462.1(ENSG00000293064):​n.285+961A>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 0.107 in 152,156 control chromosomes in the GnomAD database, including 2,528 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 0.11 (2528 hom., cov: 32)
• Consequence: ENST00000419462.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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
	ENST00000419462.1	n.285+961A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16192 AN: 152038 Hom.: 2504 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.00886

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.00594

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00898

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.107 AC: 16270 AN: 152156 Hom.: 2528 Cov.: 32 AF XY: 0.105 AC XY: 7783 AN XY: 74394

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.0535

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.00888

Gnomad4 SAS AF: 0.0188

Gnomad4 FIN AF: 0.00594

Gnomad4 NFE AF: 0.00898

Gnomad4 OTH AF: 0.0909

Alfa AF: 0.0318 Hom.: 480

Bravo AF: 0.122

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16867579; hg19: chr8-102375267;