2-106207196-C-T

Variant names:

• chr2-106207196-C-T
• rs13006272
• ENST00000771335.1:n.143+7574C>T

Variant summary

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

The ENST00000771335.1(ENSG00000300396):​n.143+7574C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,222 control chromosomes in the GnomAD database, including 47,774 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 0.79 (47774 hom., cov: 34)
• Consequence: ENSG00000300396 ENST00000771335.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 5 publications found

Genes affected

ENSG00000300396 (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 (NFE) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771335.1. 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
	ENSG00000300396	ENST00000771335.1		n.143+7574C>T		intron	N/A
	ENSG00000273595	ENST00000611308.1	TSL:6	n.-198C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119923 AN: 152104 Hom.: 47772 Cov.: 34

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.788 AC: 119950 AN: 152222 Hom.: 47774 Cov.: 34 AF XY: 0.784 AC XY: 58349 AN XY: 74424

African (AFR) AF: 0.725 AC: 30100 AN: 41518

American (AMR) AF: 0.715 AC: 10937 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3207 AN: 3472

East Asian (EAS) AF: 0.606 AC: 3137 AN: 5176

South Asian (SAS) AF: 0.751 AC: 3619 AN: 4822

European-Finnish (FIN) AF: 0.788 AC: 8352 AN: 10600

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57851 AN: 68024

Other (OTH) AF: 0.807 AC: 1707 AN: 2114

Alfa AF: 0.826 Hom.: 95393

Bravo AF: 0.774

Asia WGS AF: 0.629 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.67
DANN	Benign	0.33
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs13006272; hg19: chr2-106823652;