rs2468680

Variant names:

• chr8-139508977-G-A
• rs2468680
• ENST00000611315.1:n.-6C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-139508977-G-A
• chr8-139508977-G-C
• chr8-139508977-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000611315.1(ENSG00000275078):​n.-6C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,116 control chromosomes in the GnomAD database, including 6,966 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 0.29 (6963 hom., cov: 33)
  • Exomes 𝑓: 0.38 (3 hom.)
• Consequence: ENSG00000275078 ENST00000611315.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 4 publications found

Genes affected

ENSG00000275078 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611315.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000275078	ENST00000611315.1	TSL:6	n.-6C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44109 AN: 151974 Hom.: 6956 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.308

GnomAD4 exome AF: 0.375 AC: 9 AN: 24 Hom.: 3 Cov.: 0 AF XY: 0.563 AC XY: 9 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.400 AC: 8 AN: 20

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.290 AC: 44141 AN: 152092 Hom.: 6963 Cov.: 33 AF XY: 0.299 AC XY: 22236 AN XY: 74330

African (AFR) AF: 0.237 AC: 9847 AN: 41478

American (AMR) AF: 0.354 AC: 5418 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3468

East Asian (EAS) AF: 0.674 AC: 3478 AN: 5158

South Asian (SAS) AF: 0.359 AC: 1733 AN: 4824

European-Finnish (FIN) AF: 0.338 AC: 3569 AN: 10568

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17979 AN: 67988

Other (OTH) AF: 0.309 AC: 652 AN: 2108

Alfa AF: 0.273 Hom.: 1118

Bravo AF: 0.292

Asia WGS AF: 0.455 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.59
DANN	Benign	0.53
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2468680;

hg19: chr8-140521220;