chr7-150353338-T-C

Variant names:

• chr7-150353338-T-C
• rs10259796
• ENST00000782368.1:n.257-3961T>C

Variant summary

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

The ENST00000782368.1(ENSG00000301866):​n.257-3961T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,078 control chromosomes in the GnomAD database, including 4,291 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 0.23 (4291 hom., cov: 31)
• Consequence: ENSG00000301866 ENST00000782368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386
• Publications: 16 publications found

Genes affected

ENSG00000301866 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782368.1. 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
	ENSG00000301866	ENST00000782368.1		n.257-3961T>C		intron	N/A
	ENSG00000301866	ENST00000782369.1		n.240-3965T>C		intron	N/A
	ENSG00000301866	ENST00000782370.1		n.338-3961T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34640 AN: 151960 Hom.: 4293 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.228 AC: 34644 AN: 152078 Hom.: 4291 Cov.: 31 AF XY: 0.231 AC XY: 17154 AN XY: 74310

African (AFR) AF: 0.129 AC: 5369 AN: 41510

American (AMR) AF: 0.164 AC: 2516 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1081 AN: 3472

East Asian (EAS) AF: 0.282 AC: 1451 AN: 5154

South Asian (SAS) AF: 0.346 AC: 1666 AN: 4812

European-Finnish (FIN) AF: 0.279 AC: 2948 AN: 10554

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18725 AN: 67964

Other (OTH) AF: 0.212 AC: 448 AN: 2110

Alfa AF: 0.253 Hom.: 14476

Bravo AF: 0.212

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.66
PhyloP100		0.39

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: rs10259796;

hg19: chr7-150050427;