7-11914949-A-G

Variant names:

• chr7-11914949-A-G
• rs10234648
• ENST00000775347.1:n.291-8507T>C

Variant summary

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

The ENST00000775347.1(ENSG00000300984):​n.291-8507T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,162 control chromosomes in the GnomAD database, including 2,547 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 0.18 (2547 hom., cov: 32)
• Consequence: ENSG00000300984 ENST00000775347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 3 publications found

Genes affected

ENSG00000300984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775347.1. 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
	ENSG00000300984	ENST00000775347.1		n.291-8507T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27131 AN: 152044 Hom.: 2547 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.178 AC: 27149 AN: 152162 Hom.: 2547 Cov.: 32 AF XY: 0.181 AC XY: 13480 AN XY: 74376

African (AFR) AF: 0.140 AC: 5824 AN: 41528

American (AMR) AF: 0.217 AC: 3314 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3472

East Asian (EAS) AF: 0.248 AC: 1279 AN: 5162

South Asian (SAS) AF: 0.197 AC: 948 AN: 4816

European-Finnish (FIN) AF: 0.211 AC: 2231 AN: 10586

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.179 AC: 12175 AN: 67998

Other (OTH) AF: 0.189 AC: 399 AN: 2114

Alfa AF: 0.181 Hom.: 4901

Bravo AF: 0.180

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.32
PhyloP100		0.26

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: rs10234648;

hg19: chr7-11954575;