rs6945912

Variant names:

• chr7-31168632-C-T
• rs6945912
• ENST00000763545.1:n.228+30943C>T

Variant summary

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

The ENST00000763545.1(ENSG00000286487):​n.228+30943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0543 in 152,056 control chromosomes in the GnomAD database, including 635 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 0.054 (635 hom., cov: 32)
• Consequence: ENSG00000286487 ENST00000763545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 0 publications found

Genes affected

ENSG00000286487 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763545.1. 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
	ENSG00000286487	ENST00000763545.1		n.228+30943C>T		intron	N/A
	ENSG00000286487	ENST00000763546.1		n.177+30943C>T		intron	N/A
	ENSG00000286487	ENST00000763547.1		n.241+30943C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0543 AC: 8254 AN: 151938 Hom.: 637 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0197

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.00577

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00293

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0543 AC: 8263 AN: 152056 Hom.: 635 Cov.: 32 AF XY: 0.0530 AC XY: 3939 AN XY: 74350

African (AFR) AF: 0.175 AC: 7236 AN: 41450

American (AMR) AF: 0.0196 AC: 300 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.0452 AC: 234 AN: 5172

South Asian (SAS) AF: 0.0286 AC: 138 AN: 4820

European-Finnish (FIN) AF: 0.00577 AC: 61 AN: 10566

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00293 AC: 199 AN: 67982

Other (OTH) AF: 0.0431 AC: 91 AN: 2110

Alfa AF: 0.0265 Hom.: 84

Bravo AF: 0.0611

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		-0.21

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: rs6945912;

hg19: chr7-31208246;