rs2046210

chr6-151627231-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The XR_007059816.1(LOC124901435):n.657G>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 0.407 in 151,962 control chromosomes in the GnomAD database, including 14,125 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.41 (14125 hom., cov: 32)
• Consequence: LOC124901435 XR_007059816.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter P:1 B:1
• Conservation: PhyloP100: -0.156

Genes affected

LOC124901435 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 6-151627231-G-A is Benign according to our data. Variant chr6-151627231-G-A is described in ClinVar as [Benign]. Clinvar id is 155877.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901435	XR_007059816.1	n.657G>A		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61735 AN: 151844 Hom.: 14105 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.407 AC: 61788 AN: 151962 Hom.: 14125 Cov.: 32 AF XY: 0.399 AC XY: 29605 AN XY: 74278

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.419

Alfa AF: 0.359 Hom.: 13856

Bravo AF: 0.424

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Estrogen resistance syndrome Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

Department of Breast and Endocrine Surgery, Kumamoto University

Mar 01, 2014

- -

not specified Benign:1

Benign, criteria provided, single submitter

research

H3Africa Consortium

Oct 28, 2020

While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.729, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046210; hg19: chr6-151948366; COSMIC: COSV53317094;