rs16908145

Variant names:

• chr8-138025730-T-A
• rs16908145
• ENST00000518973.1:n.514+57327A>T

Your query was ambiguous. Multiple possible variants found:

• chr8-138025730-T-A
• chr8-138025730-T-C
• chr8-138025730-T-G

Variant summary

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

The ENST00000518973.1(ENSG00000253288):​n.514+57327A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0356 in 152,220 control chromosomes in the GnomAD database, including 120 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 0.036 (120 hom., cov: 32)
• Consequence: ENSG00000253288 ENST00000518973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455
• Publications: 2 publications found

Genes affected

ENSG00000253288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC401478	NR_161374.1	n.573+14609A>T		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253288	ENST00000518973.1	n.514+57327A>T		intron_variant	Intron 1 of 2	2
ENSG00000253288	ENST00000657186.1	n.601+57327A>T		intron_variant	Intron 1 of 2
ENSG00000254361	ENST00000716518.1	n.621+6049T>A		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.0355 AC: 5400 AN: 152102 Hom.: 119 Cov.: 32

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0432

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0470

Gnomad FIN AF: 0.00820

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0356 AC: 5419 AN: 152220 Hom.: 120 Cov.: 32 AF XY: 0.0341 AC XY: 2540 AN XY: 74450

African (AFR) AF: 0.0675 AC: 2801 AN: 41522

American (AMR) AF: 0.0432 AC: 660 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.0471 AC: 227 AN: 4822

European-Finnish (FIN) AF: 0.00820 AC: 87 AN: 10614

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0213 AC: 1448 AN: 68004

Other (OTH) AF: 0.0293 AC: 62 AN: 2116

Alfa AF: 0.00871 Hom.: 1

Bravo AF: 0.0402

Asia WGS AF: 0.0260 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.6
DANN	Benign	0.41
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs16908145; hg19: chr8-139037973;