rs2052089

chr7-66664967-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110037.1(LOC100996437):n.109-2431T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,182 control chromosomes in the GnomAD database, including 44,585 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 0.76 (44585 hom., cov: 33)
• Consequence: LOC100996437 NR_110037.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100996437	NR_110037.1	n.109-2431T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000693151.1	n.114+10341T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116157 AN: 152064 Hom.: 44540 Cov.: 33

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.764 AC: 116263 AN: 152182 Hom.: 44585 Cov.: 33 AF XY: 0.768 AC XY: 57117 AN XY: 74404

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.770

Alfa AF: 0.751 Hom.: 5348

Bravo AF: 0.770

Asia WGS AF: 0.703 AC: 2445 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	1.4
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2052089; hg19: chr7-66129954;