7-150980992-A-G

Variant names:

• chr7-150980992-A-G
• rs2373885
• ENST00000815006.1:n.300+6T>C

Variant summary

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

The ENST00000815006.1(ENSG00000306061):​n.300+6T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,006 control chromosomes in the GnomAD database, including 11,349 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 0.36 (11349 hom., cov: 33)
• Consequence: ENSG00000306061 ENST00000815006.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 10 publications found

Genes affected

ENSG00000306061 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815006.1. 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
	ENSG00000306061	ENST00000815006.1		n.300+6T>C		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54800 AN: 151888 Hom.: 11316 Cov.: 33

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.361 AC: 54881 AN: 152006 Hom.: 11349 Cov.: 33 AF XY: 0.369 AC XY: 27386 AN XY: 74292

African (AFR) AF: 0.509 AC: 21086 AN: 41446

American (AMR) AF: 0.383 AC: 5853 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1121 AN: 3472

East Asian (EAS) AF: 0.752 AC: 3881 AN: 5158

South Asian (SAS) AF: 0.428 AC: 2064 AN: 4818

European-Finnish (FIN) AF: 0.303 AC: 3206 AN: 10576

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16605 AN: 67928

Other (OTH) AF: 0.344 AC: 726 AN: 2108

Alfa AF: 0.287 Hom.: 26449

Bravo AF: 0.378

Asia WGS AF: 0.586 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		-0.15

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: rs2373885;

hg19: chr7-150678080;