rs2888830

Positions:

• chr7-91286039-G-A
• chr7-91286039-G-T

Variant summary

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

The XR_007060425.1(LOC124901695):​n.126+1268C>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 0.645 in 152,048 control chromosomes in the GnomAD database, including 31,754 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 0.64 (31754 hom., cov: 32)
• Consequence: LOC124901695 XR_007060425.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

Genes affected

LOC124901695 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901695	XR_007060425.1	n.126+1268C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97961 AN: 151930 Hom.: 31744 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.645 AC: 97998 AN: 152048 Hom.: 31754 Cov.: 32 AF XY: 0.643 AC XY: 47806 AN XY: 74306

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.644

Alfa AF: 0.674 Hom.: 32821

Bravo AF: 0.649

Asia WGS AF: 0.559 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2888830; hg19: chr7-90915354;