chr6-166969587-G-A

Variant names:

• chr6-166969587-G-A
• rs9355610
• NR_188001.1:n.808+39C>T

Variant summary

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

The NR_188001.1(LOC105378120):​n.808+39C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,022 control chromosomes in the GnomAD database, including 12,112 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 0.39 (12111 hom., cov: 33)
  • Exomes 𝑓: 0.26 (1 hom.)
• Consequence: LOC105378120 NR_188001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 61 publications found

Genes affected

LOC105378120 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188001.1. 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
	LOC105378120	NR_188001.1		n.808+39C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227598	ENST00000444102.1	TSL:5	n.*39C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59405 AN: 151862 Hom.: 12097 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.421

GnomAD4 exome AF: 0.262 AC: 11 AN: 42 Hom.: 1 Cov.: 0 AF XY: 0.313 AC XY: 5 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) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 6 AN: 30

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.391 AC: 59460 AN: 151980 Hom.: 12111 Cov.: 33 AF XY: 0.400 AC XY: 29722 AN XY: 74270

African (AFR) AF: 0.391 AC: 16175 AN: 41412

American (AMR) AF: 0.504 AC: 7698 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1490 AN: 3472

East Asian (EAS) AF: 0.531 AC: 2748 AN: 5174

South Asian (SAS) AF: 0.602 AC: 2905 AN: 4826

European-Finnish (FIN) AF: 0.392 AC: 4130 AN: 10538

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22922 AN: 67966

Other (OTH) AF: 0.426 AC: 897 AN: 2104

Alfa AF: 0.356 Hom.: 40404

Bravo AF: 0.399

Asia WGS AF: 0.559 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		0.087

Splicing

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

Other links and lift over

dbSNP: rs9355610; hg19: chr6-167383075; COSMIC: COSV71411264;