rs7611217

Variant names:

• chr3-143125611-G-A
• rs7611217
• ENST00000483262.1:n.215+2035G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-143125611-G-A
• chr3-143125611-G-C

Variant summary

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

The ENST00000483262.1(ENSG00000241679):​n.215+2035G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,156 control chromosomes in the GnomAD database, including 40,502 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 0.72 (40502 hom., cov: 33)
• Consequence: ENSG00000241679 ENST00000483262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000241679	ENST00000483262.1	TSL:3	n.215+2035G>A		intron	N/A
	ENSG00000241679	ENST00000840528.1		n.361-26513G>A		intron	N/A
	ENSG00000241679	ENST00000840529.1		n.376-6107G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109733 AN: 152038 Hom.: 40435 Cov.: 33

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.722 AC: 109862 AN: 152156 Hom.: 40502 Cov.: 33 AF XY: 0.726 AC XY: 53987 AN XY: 74384

African (AFR) AF: 0.884 AC: 36694 AN: 41518

American (AMR) AF: 0.730 AC: 11164 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2196 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3818 AN: 5178

South Asian (SAS) AF: 0.647 AC: 3117 AN: 4816

European-Finnish (FIN) AF: 0.668 AC: 7073 AN: 10588

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43420 AN: 67974

Other (OTH) AF: 0.707 AC: 1495 AN: 2114

Alfa AF: 0.672 Hom.: 51990

Bravo AF: 0.734

Asia WGS AF: 0.721 AC: 2508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7611217; hg19: chr3-142844453;