rs885618

Variant names:

• chr9-126520078-G-A
• rs885618
• ENST00000624132.1:n.1239G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-126520078-G-A
• chr9-126520078-G-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_930358.4(LOC105376276):​n.1945G>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 0.225 in 152,188 control chromosomes in the GnomAD database, including 5,010 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 0.23 (5010 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: LOC105376276 XR_930358.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.05
• Publications: 1 publications found

Genes affected

ENSG00000279137 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624132.1. 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
	ENSG00000279137	ENST00000624132.1	TSL:6	n.1239G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000295036	ENST00000727533.1		n.370+5405C>T		intron	N/A
	ENSG00000233721	ENST00000727649.1		n.259+3397G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34213 AN: 152054 Hom.: 4992 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.229

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

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: 0.00 AC: 0 AN: 2

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.125 AC: 1 AN: 8

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.225 AC: 34275 AN: 152172 Hom.: 5010 Cov.: 32 AF XY: 0.228 AC XY: 16967 AN XY: 74396

African (AFR) AF: 0.328 AC: 13603 AN: 41486

American (AMR) AF: 0.306 AC: 4682 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 821 AN: 3472

East Asian (EAS) AF: 0.657 AC: 3397 AN: 5168

South Asian (SAS) AF: 0.147 AC: 708 AN: 4820

European-Finnish (FIN) AF: 0.136 AC: 1437 AN: 10594

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8988 AN: 68014

Other (OTH) AF: 0.235 AC: 497 AN: 2114

Alfa AF: 0.174 Hom.: 2404

Bravo AF: 0.250

Asia WGS AF: 0.382 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	17
DANN	Benign	0.73
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs885618; hg19: chr9-129282357;