ENST00000661243.1:n.1354-847G>A

Variant names:

• chr7-69146973-C-T
• rs6945541
• ENST00000661243.1:n.1354-847G>A

Variant summary

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

The ENST00000661243.1(ENSG00000225718):​n.1354-847G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,062 control chromosomes in the GnomAD database, including 36,735 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 0.68 (36735 hom., cov: 33)
• Consequence: ENSG00000225718 ENST00000661243.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 21 publications found

Genes affected

ENSG00000225718 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375343	XR_927647.1	n.88-847G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225718	ENST00000661243.1	n.1354-847G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103127 AN: 151944 Hom.: 36681 Cov.: 33

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.679 AC: 103240 AN: 152062 Hom.: 36735 Cov.: 33 AF XY: 0.685 AC XY: 50916 AN XY: 74304

African (AFR) AF: 0.877 AC: 36406 AN: 41504

American (AMR) AF: 0.672 AC: 10266 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1775 AN: 3466

East Asian (EAS) AF: 0.970 AC: 5028 AN: 5182

South Asian (SAS) AF: 0.735 AC: 3547 AN: 4828

European-Finnish (FIN) AF: 0.627 AC: 6615 AN: 10542

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37477 AN: 67958

Other (OTH) AF: 0.639 AC: 1345 AN: 2106

Alfa AF: 0.613 Hom.: 24053

Bravo AF: 0.692

Asia WGS AF: 0.837 AC: 2905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.74
DANN	Benign	0.76
PhyloP100		-0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6945541; hg19: chr7-68611960;