rs6801610

chr3-143129525-A-G

Variant summary

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

The ENST00000483262.1(ENSG00000241679):n.216-2193A>G 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 0.547 in 151,980 control chromosomes in the GnomAD database, including 23,649 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 0.55 (23649 hom., cov: 32)
• Consequence: ENST00000483262.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374137	XR_924554.3	n.138-1456T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000483262.1	n.216-2193A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83063 AN: 151862 Hom.: 23610 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.547 AC: 83162 AN: 151980 Hom.: 23649 Cov.: 32 AF XY: 0.548 AC XY: 40739 AN XY: 74278

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.543

Alfa AF: 0.519 Hom.: 4699

Bravo AF: 0.549

Asia WGS AF: 0.471 AC: 1640 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	11
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6801610; hg19: chr3-142848367;