rs10521153

Variant names:

• chr16-35911508-A-C
• rs10521153
• ENST00000802595.1:n.247-7728A>C

Variant summary

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

The ENST00000802595.1(ENSG00000304337):​n.247-7728A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.042 in 152,312 control chromosomes in the GnomAD database, including 377 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 0.042 (377 hom., cov: 32)
• Consequence: ENSG00000304337 ENST00000802595.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 1 publications found

Genes affected

ENSG00000304337 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304337	ENST00000802595.1	n.247-7728A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0419 AC: 6373 AN: 152192 Hom.: 375 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0218

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00704

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00306

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0420 AC: 6404 AN: 152312 Hom.: 377 Cov.: 32 AF XY: 0.0415 AC XY: 3092 AN XY: 74492

African (AFR) AF: 0.135 AC: 5596 AN: 41536

American (AMR) AF: 0.0218 AC: 334 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0340 AC: 118 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5194

South Asian (SAS) AF: 0.00704 AC: 34 AN: 4828

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10624

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00307 AC: 209 AN: 68030

Other (OTH) AF: 0.0303 AC: 64 AN: 2114

Alfa AF: 0.0387 Hom.: 31

Bravo AF: 0.0475

Asia WGS AF: 0.0130 AC: 46 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.47
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs10521153; hg19: chr16-35145879;