chr16-7969609-T-G

Position:

• chr16-7969609-T-G

Variant summary

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

The ENST00000670665.1(ENSG00000260289):​n.484+8220A>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 0.196 in 152,170 control chromosomes in the GnomAD database, including 3,195 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 0.20 (3195 hom., cov: 32)
• Consequence: ENST00000670665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833

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 (NFE) allele frequency at 95% confidence interval = 0.238 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
	ENST00000670665.1	n.484+8220A>C		intron_variant, non_coding_transcript_variant
	ENST00000567103.2	n.381+37536A>C		intron_variant, non_coding_transcript_variant		5
	ENST00000654046.1	n.414+37536A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29792 AN: 152050 Hom.: 3197 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.196 AC: 29782 AN: 152170 Hom.: 3195 Cov.: 32 AF XY: 0.194 AC XY: 14446 AN XY: 74398

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.211

Alfa AF: 0.213 Hom.: 2724

Bravo AF: 0.196

Asia WGS AF: 0.189 AC: 657 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	0.18
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395593; hg19: chr16-8019611;