rs549043

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648652.1(ENSG00000253634):​n.1052+9684C>T variant causes a intron, non coding transcript 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: ENST00000648652.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105375639	XR_007061005.1	n.425+10666C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648652.1	n.1052+9684C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0655

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0858

Gnomad4 NFE AF: 0.0879

Gnomad4 OTH AF: 0.182

Alfa AF: 0.121 Hom.: 986

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs549043; hg19: chr8-93502300;