rs12596341

Positions:

• chr16-85933434-C-A

Variant summary

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

The ENST00000646214.1(ENSG00000285163):​n.77+8374C>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 0.0802 in 152,186 control chromosomes in the GnomAD database, including 672 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 0.080 (672 hom., cov: 31)
• Consequence: ENST00000646214.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.776

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 (EAS) allele frequency at 95% confidence interval = 0.164 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+8374C>A		intron_variant, non_coding_transcript_variant
	ENST00000645383.1	n.393+1160C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12202 AN: 152068 Hom.: 669 Cov.: 31

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.0802 AC: 12201 AN: 152186 Hom.: 672 Cov.: 31 AF XY: 0.0789 AC XY: 5867 AN XY: 74400

Gnomad4 AFR AF: 0.0202

Gnomad4 AMR AF: 0.0785

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0625

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0985

Alfa AF: 0.0859 Hom.: 98

Bravo AF: 0.0791

Asia WGS AF: 0.118 AC: 410 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	2.1
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12596341; hg19: chr16-85967040;