7-150344747-T-G

Variant names:

• chr7-150344747-T-G
• rs6964110
• ENST00000782368.1:n.256+1106T>G

Variant summary

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

The ENST00000782368.1(ENSG00000301866):​n.256+1106T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,650 control chromosomes in the GnomAD database, including 5,304 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 0.26 (5304 hom., cov: 31)
• Consequence: ENSG00000301866 ENST00000782368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.291 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.256+1106T>G		intron	N/A
	ENSG00000301866	ENST00000782369.1		n.239+1106T>G		intron	N/A
	ENSG00000301866	ENST00000782370.1		n.235+1106T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39745 AN: 151538 Hom.: 5300 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.262 AC: 39778 AN: 151650 Hom.: 5304 Cov.: 31 AF XY: 0.261 AC XY: 19355 AN XY: 74090

African (AFR) AF: 0.288 AC: 11907 AN: 41294

American (AMR) AF: 0.167 AC: 2555 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1478 AN: 5154

South Asian (SAS) AF: 0.304 AC: 1459 AN: 4804

European-Finnish (FIN) AF: 0.251 AC: 2629 AN: 10454

Middle Eastern (MID) AF: 0.252 AC: 73 AN: 290

European-Non Finnish (NFE) AF: 0.261 AC: 17701 AN: 67908

Other (OTH) AF: 0.236 AC: 498 AN: 2108

Alfa AF: 0.146 Hom.: 266

Bravo AF: 0.257

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.60
PhyloP100		0.29

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: rs6964110;

hg19: chr7-150041836;