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 ENST00000624132.1(ENSG00000279137):​n.1239G>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: ENSG00000279137 ENST00000624132.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376276	XR_930358.4	n.1945G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279137	ENST00000624132.1	n.1239G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000295036	ENST00000727533.1	n.370+5405C>T		intron_variant	Intron 2 of 2
ENSG00000233721	ENST00000727649.1	n.259+3397G>A		intron_variant	Intron 2 of 2

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 v4.3

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;