ENST00000836569.1:n.295-18723T>G

Variant names:

• chr7-56138165-T-G
• rs816236
• ENST00000836569.1:n.295-18723T>G

Variant summary

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

The ENST00000836569.1(ENSG00000308815):​n.295-18723T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,138 control chromosomes in the GnomAD database, including 1,992 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 0.15 (1992 hom., cov: 33)
• Consequence: ENSG00000308815 ENST00000836569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 3 publications found

Genes affected

ENSG00000308815 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308815	ENST00000836569.1	n.295-18723T>G		intron_variant	Intron 1 of 1
ENSG00000308815	ENST00000836570.1	n.295-8972T>G		intron_variant	Intron 1 of 2
ENSG00000308815	ENST00000836571.1	n.288-6177T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22923 AN: 152020 Hom.: 1991 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.151 AC: 22948 AN: 152138 Hom.: 1992 Cov.: 33 AF XY: 0.156 AC XY: 11574 AN XY: 74364

African (AFR) AF: 0.134 AC: 5562 AN: 41508

American (AMR) AF: 0.145 AC: 2211 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3470

East Asian (EAS) AF: 0.452 AC: 2342 AN: 5178

South Asian (SAS) AF: 0.133 AC: 642 AN: 4826

European-Finnish (FIN) AF: 0.193 AC: 2040 AN: 10576

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9344 AN: 67998

Other (OTH) AF: 0.145 AC: 306 AN: 2110

Alfa AF: 0.134 Hom.: 1771

Bravo AF: 0.148

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.8
DANN	Benign	0.28
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs816236; hg19: chr7-56205858;