rs9355610

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-166969587-G-A
• chr6-166969587-G-C
• chr6-166969587-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105378120 (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 (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378120	NR_188001.1	n.808+39C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227598	ENST00000444102.1	n.*39C>T		downstream_gene_variant		5

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

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.250

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

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.426

Alfa AF: 0.352 Hom.: 18295

Bravo AF: 0.399

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	0.56

Splicing

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

Publications

LitVar

Other links and lift over

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