rs611525

Positions:

• chr6-168686862-G-A

Variant summary

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

The XR_007059886.1(LOC124901468):​n.1639G>A 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 0.955 in 152,310 control chromosomes in the GnomAD database, including 69,521 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 0.96 (69521 hom., cov: 33)
• Consequence: LOC124901468 XR_007059886.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670

Genes affected

LOC124901468 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901468	XR_007059886.1	n.1639G>A		non_coding_transcript_exon_variant	4/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145381 AN: 152192 Hom.: 69476 Cov.: 33

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.957

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

GnomAD4 genome AF: 0.955 AC: 145486 AN: 152310 Hom.: 69521 Cov.: 33 AF XY: 0.954 AC XY: 71019 AN XY: 74458

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.927

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.956

Alfa AF: 0.950 Hom.: 10785

Bravo AF: 0.957

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs611525; hg19: chr6-169086978;