rs7950547

Variant names:

• chr11-69231321-T-C
• rs7950547
• ENST00000779509.1:n.139-17040T>C

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.139-17040T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,916 control chromosomes in the GnomAD database, including 34,912 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 0.67 (34912 hom., cov: 29)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 5 publications found

Genes affected

ENSG00000301530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369367	NR_188530.1	n.1175+295A>G		intron_variant	Intron 3 of 3
LOC105369367	NR_188531.1	n.509+295A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301530	ENST00000779509.1	n.139-17040T>C		intron_variant	Intron 1 of 3
ENSG00000301550	ENST00000779653.1	n.378+295A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101563 AN: 151798 Hom.: 34867 Cov.: 29

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.669 AC: 101664 AN: 151916 Hom.: 34912 Cov.: 29 AF XY: 0.669 AC XY: 49623 AN XY: 74210

African (AFR) AF: 0.827 AC: 34259 AN: 41426

American (AMR) AF: 0.553 AC: 8451 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2530 AN: 3470

East Asian (EAS) AF: 0.463 AC: 2377 AN: 5136

South Asian (SAS) AF: 0.580 AC: 2796 AN: 4820

European-Finnish (FIN) AF: 0.666 AC: 7024 AN: 10554

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42149 AN: 67936

Other (OTH) AF: 0.673 AC: 1415 AN: 2104

Alfa AF: 0.637 Hom.: 33108

Bravo AF: 0.670

Asia WGS AF: 0.611 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.34
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7950547; hg19: chr11-68998788;