rs1109670

Variant names:

• chr2-9109909-C-A
• rs1109670
• ENST00000740123.1:n.85+364G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-9109909-C-A
• chr2-9109909-C-G

Variant summary

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

The ENST00000740123.1(ENSG00000296532):​n.85+364G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,240 control chromosomes in the GnomAD database, including 6,077 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 0.28 (6076 hom., cov: 34)
  • Exomes 𝑓: 0.23 (1 hom.)
• Consequence: ENSG00000296532 ENST00000740123.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 20 publications found

Genes affected

ENSG00000296532 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373414	NR_187857.1	n.*50C>A		downstream_gene_variant
LOC105373414	NR_187858.1	n.*50C>A		downstream_gene_variant
LOC105373414	NR_187859.1	n.*50C>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296532	ENST00000740123.1	n.85+364G>T		intron_variant	Intron 1 of 2
ENSG00000296532	ENST00000740127.1	n.82+364G>T		intron_variant	Intron 1 of 2
ENSG00000296532	ENST00000740128.1	n.83+364G>T		intron_variant	Intron 1 of 2
ENSG00000261104	ENST00000565044.1	n.*44C>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42180 AN: 152014 Hom.: 6062 Cov.: 34

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.227 AC: 25 AN: 110 Hom.: 1 Cov.: 0 AF XY: 0.289 AC XY: 22 AN XY: 76

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) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.357 AC: 5 AN: 14

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.200 AC: 16 AN: 80

Other (OTH) AF: 0.250 AC: 3 AN: 12

GnomAD4 genome AF: 0.278 AC: 42218 AN: 152130 Hom.: 6076 Cov.: 34 AF XY: 0.283 AC XY: 21074 AN XY: 74362

African (AFR) AF: 0.286 AC: 11854 AN: 41494

American (AMR) AF: 0.335 AC: 5115 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 959 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1578 AN: 5178

South Asian (SAS) AF: 0.491 AC: 2367 AN: 4824

European-Finnish (FIN) AF: 0.237 AC: 2507 AN: 10584

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16925 AN: 67982

Other (OTH) AF: 0.292 AC: 617 AN: 2110

Alfa AF: 0.265 Hom.: 12013

Bravo AF: 0.281

Asia WGS AF: 0.419 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1109670; hg19: chr2-9250038;