chr3-106470253-T-C

Variant names:

• chr3-106470253-T-C
• rs7431430
• ENST00000668075.2:n.211-20156A>G

Variant summary

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

The ENST00000668075.2(ENSG00000291293):​n.211-20156A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,080 control chromosomes in the GnomAD database, including 6,200 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 0.28 (6200 hom., cov: 32)
• Consequence: ENSG00000291293 ENST00000668075.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 4 publications found

Genes affected

ENSG00000291293 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929485	XR_007095992.1	n.1049+30464A>G		intron_variant	Intron 5 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291293	ENST00000668075.2	n.211-20156A>G		intron_variant	Intron 2 of 2
ENSG00000291293	ENST00000836909.1	n.97+30464A>G		intron_variant	Intron 1 of 3
ENSG00000291293	ENST00000836910.1	n.100+30464A>G		intron_variant	Intron 1 of 4
ENSG00000291293	ENST00000836911.1	n.185+14905A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43021 AN: 151962 Hom.: 6193 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.283 AC: 43052 AN: 152080 Hom.: 6200 Cov.: 32 AF XY: 0.283 AC XY: 21022 AN XY: 74322

African (AFR) AF: 0.286 AC: 11871 AN: 41492

American (AMR) AF: 0.281 AC: 4289 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3466

East Asian (EAS) AF: 0.232 AC: 1203 AN: 5184

South Asian (SAS) AF: 0.303 AC: 1462 AN: 4818

European-Finnish (FIN) AF: 0.236 AC: 2490 AN: 10564

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19721 AN: 67960

Other (OTH) AF: 0.285 AC: 602 AN: 2112

Alfa AF: 0.292 Hom.: 19566

Bravo AF: 0.287

Asia WGS AF: 0.244 AC: 850 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.54
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs7431430; hg19: chr3-106189100;