ENST00000412996.2:n.113+7005C>T

Variant names:

• chr7-47072072-G-A
• rs36021960
• ENST00000412996.2:n.113+7005C>T

Variant summary

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

The ENST00000412996.2(ENSG00000229192):​n.113+7005C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 152,046 control chromosomes in the GnomAD database, including 834 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 0.093 (834 hom., cov: 32)
• Consequence: ENSG00000229192 ENST00000412996.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447
• Publications: 0 publications found

Genes affected

ENSG00000229192 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375268	XR_927249.1	n.121+7005C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229192	ENST00000412996.2	n.113+7005C>T		intron_variant	Intron 2 of 4	3
ENSG00000229192	ENST00000455078.5	n.37+7005C>T		intron_variant	Intron 1 of 3	3
ENSG00000229192	ENST00000739918.1	n.125+7005C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0936 AC: 14218 AN: 151928 Hom.: 833 Cov.: 32

Gnomad AFR AF: 0.0303

Gnomad AMI AF: 0.0848

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0625

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.0935 AC: 14216 AN: 152046 Hom.: 834 Cov.: 32 AF XY: 0.0917 AC XY: 6815 AN XY: 74300

African (AFR) AF: 0.0303 AC: 1256 AN: 41494

American (AMR) AF: 0.108 AC: 1645 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5164

South Asian (SAS) AF: 0.0638 AC: 306 AN: 4794

European-Finnish (FIN) AF: 0.110 AC: 1165 AN: 10568

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.130 AC: 8830 AN: 67970

Other (OTH) AF: 0.120 AC: 254 AN: 2110

Alfa AF: 0.110 Hom.: 152

Bravo AF: 0.0903

Asia WGS AF: 0.0310 AC: 109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs36021960; hg19: chr7-47111670;