rs2196302

Variant names:

• chr3-5763409-G-A
• rs2196302
• ENST00000425894.2:n.461+19576G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-5763409-G-A
• chr3-5763409-G-C
• chr3-5763409-G-T

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.461+19576G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,008 control chromosomes in the GnomAD database, including 12,114 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 0.37 (12114 hom., cov: 32)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 2 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425894.2. 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
	ENSG00000229642	ENST00000425894.2	TSL:3	n.461+19576G>A		intron	N/A
	ENSG00000229642	ENST00000779001.1		n.212+66923G>A		intron	N/A
	ENSG00000229642	ENST00000779002.1		n.232+66923G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55558 AN: 151890 Hom.: 12116 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.365 AC: 55556 AN: 152008 Hom.: 12114 Cov.: 32 AF XY: 0.365 AC XY: 27146 AN XY: 74302

African (AFR) AF: 0.132 AC: 5490 AN: 41482

American (AMR) AF: 0.311 AC: 4753 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3468

East Asian (EAS) AF: 0.336 AC: 1727 AN: 5146

South Asian (SAS) AF: 0.328 AC: 1576 AN: 4812

European-Finnish (FIN) AF: 0.565 AC: 5966 AN: 10558

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33625 AN: 67956

Other (OTH) AF: 0.346 AC: 729 AN: 2108

Alfa AF: 0.448 Hom.: 10325

Bravo AF: 0.334

Asia WGS AF: 0.286 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.92
PhyloP100		-0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2196302;

hg19: chr3-5805096;