16-35281704-T-C

Variant names:

• chr16-35281704-T-C
• rs7196505
• ENST00000562572.2:n.139-2052T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000562572.2(ENSG00000260958):​n.139-2052T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,020 control chromosomes in the GnomAD database, including 43,917 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 0.76 (43917 hom., cov: 33)
• Consequence: ENSG00000260958 ENST00000562572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 5 publications found

Genes affected

ENSG00000260958 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562572.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260958	ENST00000562572.2	TSL:3	n.139-2052T>C		intron	N/A
	ENSG00000260958	ENST00000741988.1		n.513-2052T>C		intron	N/A
	ENSG00000260958	ENST00000741989.1		n.227-2052T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114683 AN: 151902 Hom.: 43871 Cov.: 33

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.755 AC: 114785 AN: 152020 Hom.: 43917 Cov.: 33 AF XY: 0.749 AC XY: 55646 AN XY: 74290

African (AFR) AF: 0.693 AC: 28741 AN: 41448

American (AMR) AF: 0.823 AC: 12554 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2551 AN: 3470

East Asian (EAS) AF: 0.628 AC: 3238 AN: 5160

South Asian (SAS) AF: 0.409 AC: 1969 AN: 4820

European-Finnish (FIN) AF: 0.816 AC: 8612 AN: 10556

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54567 AN: 67990

Other (OTH) AF: 0.761 AC: 1609 AN: 2114

Alfa AF: 0.782 Hom.: 164273

Bravo AF: 0.762

Asia WGS AF: 0.511 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.18
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7196505; hg19: chr16-34516075;