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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986858	XR_001745420.3	n.607+1106T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301866	ENST00000782368.1	n.256+1106T>G		intron_variant	Intron 1 of 1
ENSG00000301866	ENST00000782369.1	n.239+1106T>G		intron_variant	Intron 1 of 1
ENSG00000301866	ENST00000782370.1	n.235+1106T>G		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs6964110; hg19: chr7-150041836;