rs9806234

Variant names:

• chr15-74370692-A-G
• rs9806234
• ENST00000568496.3:n.4498A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-74370692-A-G
• chr15-74370692-A-T

Variant summary

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

The ENST00000568496.3(ENSG00000261821):​n.4498A>G 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 0.407 in 152,072 control chromosomes in the GnomAD database, including 15,534 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 0.41 (15532 hom., cov: 32)
  • Exomes 𝑓: 0.50 (2 hom.)
• Consequence: ENSG00000261821 ENST00000568496.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 11 publications found

Genes affected

ENSG00000261821 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568496.3. 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
	ENSG00000261821	ENST00000568496.3	TSL:2	n.4498A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000261821	ENST00000783990.1		n.689A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000261821	ENST00000783991.1		n.764A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61819 AN: 151942 Hom.: 15496 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.384

GnomAD4 exome AF: 0.500 AC: 6 AN: 12 Hom.: 2 Cov.: 0 AF XY: 0.833 AC XY: 5 AN XY: 6

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) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.407 AC: 61922 AN: 152060 Hom.: 15532 Cov.: 32 AF XY: 0.412 AC XY: 30591 AN XY: 74324

African (AFR) AF: 0.683 AC: 28304 AN: 41452

American (AMR) AF: 0.323 AC: 4935 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3468

East Asian (EAS) AF: 0.648 AC: 3345 AN: 5160

South Asian (SAS) AF: 0.610 AC: 2941 AN: 4824

European-Finnish (FIN) AF: 0.250 AC: 2646 AN: 10580

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17231 AN: 67978

Other (OTH) AF: 0.388 AC: 818 AN: 2106

Alfa AF: 0.306 Hom.: 10456

Bravo AF: 0.422

Asia WGS AF: 0.639 AC: 2222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.18
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9806234;

hg19: chr15-74663033;