rs11984645

Variant names:

• chr8-54156745-G-A
• rs11984645
• ENST00000728273.1:n.47+3532G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-54156745-G-A
• chr8-54156745-G-C

Variant summary

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

The ENST00000728273.1(ENSG00000295151):​n.47+3532G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,084 control chromosomes in the GnomAD database, including 12,875 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 0.35 (12875 hom., cov: 32)
• Consequence: ENSG00000295151 ENST00000728273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 7 publications found

Genes affected

ENSG00000295151 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 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
ENSG00000295151	ENST00000728273.1	n.47+3532G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53716 AN: 151966 Hom.: 12839 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.354 AC: 53816 AN: 152084 Hom.: 12875 Cov.: 32 AF XY: 0.362 AC XY: 26919 AN XY: 74338

African (AFR) AF: 0.632 AC: 26200 AN: 41476

American (AMR) AF: 0.327 AC: 4996 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3470

East Asian (EAS) AF: 0.718 AC: 3725 AN: 5188

South Asian (SAS) AF: 0.477 AC: 2298 AN: 4822

European-Finnish (FIN) AF: 0.295 AC: 3109 AN: 10554

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11475 AN: 67964

Other (OTH) AF: 0.349 AC: 737 AN: 2114

Alfa AF: 0.223 Hom.: 2207

Bravo AF: 0.368

Asia WGS AF: 0.585 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.55
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11984645; hg19: chr8-55069305;