16-8042169-C-T

Position:

• chr16-8042169-C-T

Variant summary

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

The ENST00000670665.1(ENSG00000260289):​n.335-34945G>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 0.929 in 152,252 control chromosomes in the GnomAD database, including 65,697 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 0.93 (65697 hom., cov: 32)
• Consequence: ENST00000670665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371070	XR_001752068.3	n.434-34945G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670665.1	n.335-34945G>A		intron_variant, non_coding_transcript_variant
	ENST00000567103.2	n.302-34945G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000654046.1	n.335-34945G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141324 AN: 152134 Hom.: 65636 Cov.: 32

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.929 AC: 141444 AN: 152252 Hom.: 65697 Cov.: 32 AF XY: 0.926 AC XY: 68955 AN XY: 74432

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.944

Gnomad4 ASJ AF: 0.911

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.934

Gnomad4 OTH AF: 0.940

Alfa AF: 0.931 Hom.: 61468

Bravo AF: 0.933

Asia WGS AF: 0.910 AC: 3164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6501061; hg19: chr16-8092171;