rs2710201

chr7-153227808-A-G

Variant summary

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

The XR_007060599.1(LOC102723686):n.2089-639A>G 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 0.209 in 152,052 control chromosomes in the GnomAD database, including 6,942 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 0.21 (6942 hom., cov: 32)
• Consequence: LOC102723686 XR_007060599.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

Genes affected

LOC102723686 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723686	XR_007060599.1	n.2089-639A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31701 AN: 151934 Hom.: 6917 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.0771

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.0642

Gnomad SAS AF: 0.0875

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.209 AC: 31774 AN: 152052 Hom.: 6942 Cov.: 32 AF XY: 0.207 AC XY: 15367 AN XY: 74354

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0452

Gnomad4 EAS AF: 0.0638

Gnomad4 SAS AF: 0.0865

Gnomad4 FIN AF: 0.0934

Gnomad4 NFE AF: 0.0567

Gnomad4 OTH AF: 0.170

Alfa AF: 0.0795 Hom.: 1471

Bravo AF: 0.229

Asia WGS AF: 0.121 AC: 422 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.42
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2710201; hg19: chr7-152924893;