rs7939734

chr11-70208839-T-Achr11-70208839-T-C

Variant summary

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

The XR_007062761.1(LOC124902705):n.293-262A>T 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 0.57 in 151,922 control chromosomes in the GnomAD database, including 24,939 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 0.57 (24939 hom., cov: 32)
• Consequence: LOC124902705 XR_007062761.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606

Genes affected

LOC124902705 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902705	XR_007062761.1	n.293-262A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86470 AN: 151806 Hom.: 24896 Cov.: 32

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.570 AC: 86567 AN: 151922 Hom.: 24939 Cov.: 32 AF XY: 0.568 AC XY: 42147 AN XY: 74232

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.558

Alfa AF: 0.566 Hom.: 3036

Bravo AF: 0.565

Asia WGS AF: 0.563 AC: 1958 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	0.13
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7939734; hg19: chr11-70054945;