rs160948

Variant names:

• chr16-76069739-C-A
• rs160948
• ENST00000808909.1:n.563-4513G>T

Variant summary

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

The ENST00000808909.1(ENSG00000260223):​n.563-4513G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,836 control chromosomes in the GnomAD database, including 10,018 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 0.33 (10018 hom., cov: 32)
• Consequence: ENSG00000260223 ENST00000808909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 0 publications found

Genes affected

ENSG00000260223 (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 (AFR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371349	XR_933750.3	n.485-4513G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260223	ENST00000808909.1	n.563-4513G>T		intron_variant	Intron 3 of 3
ENSG00000260223	ENST00000808910.1	n.543-4513G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49936 AN: 151718 Hom.: 9986 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.329 AC: 50012 AN: 151836 Hom.: 10018 Cov.: 32 AF XY: 0.321 AC XY: 23796 AN XY: 74210

African (AFR) AF: 0.566 AC: 23429 AN: 41360

American (AMR) AF: 0.210 AC: 3207 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 939 AN: 3472

East Asian (EAS) AF: 0.109 AC: 561 AN: 5162

South Asian (SAS) AF: 0.262 AC: 1256 AN: 4800

European-Finnish (FIN) AF: 0.177 AC: 1863 AN: 10554

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.262 AC: 17778 AN: 67936

Other (OTH) AF: 0.312 AC: 656 AN: 2102

Alfa AF: 0.307 Hom.: 991

Bravo AF: 0.338

Asia WGS AF: 0.229 AC: 792 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.025
DANN	Benign	0.34
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs160948; hg19: chr16-76103637;