rs549043

Variant names:

• chr8-92490072-G-A
• rs549043
• ENST00000648652.1:n.1052+9684C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-92490072-G-A
• chr8-92490072-G-T

Variant summary

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

The ENST00000648652.1(ENSG00000253634):​n.1052+9684C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,054 control chromosomes in the GnomAD database, including 5,707 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 0.21 (5707 hom., cov: 32)
• Consequence: ENSG00000253634 ENST00000648652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 2 publications found

Genes affected

ENSG00000253634 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375639	XR_007061005.1	n.425+10666C>T		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253634	ENST00000648652.1	n.1052+9684C>T		intron_variant	Intron 8 of 13
ENSG00000253634	ENST00000744168.1	n.397+10666C>T		intron_variant	Intron 4 of 6
ENSG00000253634	ENST00000744169.1	n.233+12288C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31619 AN: 151936 Hom.: 5677 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0655

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0879

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.208 AC: 31699 AN: 152054 Hom.: 5707 Cov.: 32 AF XY: 0.207 AC XY: 15390 AN XY: 74332

African (AFR) AF: 0.485 AC: 20103 AN: 41440

American (AMR) AF: 0.107 AC: 1640 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0655 AC: 227 AN: 3466

East Asian (EAS) AF: 0.285 AC: 1471 AN: 5160

South Asian (SAS) AF: 0.138 AC: 664 AN: 4806

European-Finnish (FIN) AF: 0.0858 AC: 909 AN: 10590

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0879 AC: 5979 AN: 67984

Other (OTH) AF: 0.182 AC: 385 AN: 2114

Alfa AF: 0.122 Hom.: 1128

Bravo AF: 0.221

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.72
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs549043; hg19: chr8-93502300;