rs7950640

Variant names:

• chr11-59096932-G-C
• rs7950640
• ENST00000821715.1:n.725C>G

Your query was ambiguous. Multiple possible variants found:

• chr11-59096932-G-C
• chr11-59096932-G-T

Variant summary

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

The ENST00000821715.1(ENSG00000255240):​n.725C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,072 control chromosomes in the GnomAD database, including 15,768 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 0.45 (15768 hom., cov: 32)
• Consequence: ENSG00000255240 ENST00000821715.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 3 publications found

Genes affected

ENSG00000255240 (HGNC:58086):

LOC105369315 (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 (AMR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821715.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255240	ENST00000821715.1		n.725C>G		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000255240	ENST00000821716.1		n.728C>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000255240	ENST00000821647.1		n.214+5233C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68495 AN: 151954 Hom.: 15758 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.451 AC: 68541 AN: 152072 Hom.: 15768 Cov.: 32 AF XY: 0.453 AC XY: 33701 AN XY: 74342

African (AFR) AF: 0.500 AC: 20744 AN: 41458

American (AMR) AF: 0.533 AC: 8148 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1364 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1791 AN: 5156

South Asian (SAS) AF: 0.349 AC: 1685 AN: 4830

European-Finnish (FIN) AF: 0.482 AC: 5089 AN: 10568

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28159 AN: 67984

Other (OTH) AF: 0.470 AC: 990 AN: 2108

Alfa AF: 0.281 Hom.: 637

Bravo AF: 0.458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.42
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs7950640; hg19: chr11-58864405;