16-7997956-A-G

Position:

• chr16-7997956-A-G

Variant summary

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

The ENST00000670665.1(ENSG00000260289):​n.414+9189T>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 0.0323 in 152,354 control chromosomes in the GnomAD database, including 111 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 0.032 (111 hom., cov: 33)
• Consequence: ENST00000670665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371070	XR_001752068.3	n.513+9189T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000670665.1	n.414+9189T>C		intron_variant, non_coding_transcript_variant
	ENST00000567103.2	n.381+9189T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000654046.1	n.414+9189T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0322 AC: 4902 AN: 152236 Hom.: 110 Cov.: 33

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0180

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0254

Gnomad OTH AF: 0.0334

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

GnomAD4 genome AF: 0.0323 AC: 4918 AN: 152354 Hom.: 111 Cov.: 33 AF XY: 0.0335 AC XY: 2496 AN XY: 74506

Gnomad4 AFR AF: 0.0336

Gnomad4 AMR AF: 0.0283

Gnomad4 ASJ AF: 0.0450

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0578

Gnomad4 FIN AF: 0.0180

Gnomad4 NFE AF: 0.0254

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0289 Hom.: 29

Bravo AF: 0.0330

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.041
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1567147; hg19: chr16-8047958;