rs6801610

Variant names:

• chr3-143129525-A-G
• rs6801610
• ENST00000483262.1:n.216-2193A>G

Variant summary

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

The ENST00000483262.1(ENSG00000241679):​n.216-2193A>G variant causes a intron 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: ENSG00000241679 ENST00000483262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 0 publications found

Genes affected

ENSG00000241679 (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 = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000483262.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000241679	ENST00000483262.1	TSL:3	n.216-2193A>G		intron	N/A
	ENSG00000241679	ENST00000840528.1		n.361-22599A>G		intron	N/A
	ENSG00000241679	ENST00000840529.1		n.376-2193A>G		intron	N/A

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

African (AFR) AF: 0.724 AC: 29993 AN: 41434

American (AMR) AF: 0.481 AC: 7340 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1702 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1659 AN: 5164

South Asian (SAS) AF: 0.517 AC: 2493 AN: 4820

European-Finnish (FIN) AF: 0.529 AC: 5575 AN: 10536

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32589 AN: 67974

Other (OTH) AF: 0.543 AC: 1147 AN: 2114

Alfa AF: 0.510 Hom.: 7897

Bravo AF: 0.549

Asia WGS AF: 0.471 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6801610; hg19: chr3-142848367;