rs9494335

Variant names:

• chr6-135690726-A-G
• rs9494335
• ENST00000421378.4:n.1522A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-135690726-A-G
• chr6-135690726-A-T

Variant summary

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

The ENST00000421378.4(AHI1-DT):​n.1522A>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 0.313 in 152,048 control chromosomes in the GnomAD database, including 7,630 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 0.31 (7630 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: AHI1-DT ENST00000421378.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 7 publications found

Genes affected

AHI1-DT (HGNC:32526): (AHI1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421378.4. 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
	AHI1-DT	NR_026805.1		n.1524A>G		non_coding_transcript_exon	Exon 4 of 4
	AHI1-DT	NR_152844.1		n.1638A>G		non_coding_transcript_exon	Exon 5 of 5
	AHI1-DT	NR_152845.1		n.1762A>G		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000421378.4	TSL:1	n.1522A>G		non_coding_transcript_exon	Exon 4 of 4
	AHI1-DT	ENST00000653664.1		n.1662A>G		non_coding_transcript_exon	Exon 5 of 5
	AHI1-DT	ENST00000655480.2		n.1566A>G		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47632 AN: 151930 Hom.: 7619 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.316

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.313 AC: 47663 AN: 152048 Hom.: 7630 Cov.: 32 AF XY: 0.311 AC XY: 23083 AN XY: 74326

African (AFR) AF: 0.270 AC: 11220 AN: 41486

American (AMR) AF: 0.352 AC: 5369 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3470

East Asian (EAS) AF: 0.406 AC: 2104 AN: 5180

South Asian (SAS) AF: 0.411 AC: 1980 AN: 4822

European-Finnish (FIN) AF: 0.198 AC: 2101 AN: 10586

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22545 AN: 67922

Other (OTH) AF: 0.317 AC: 668 AN: 2110

Alfa AF: 0.312 Hom.: 1328

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		0.15

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: rs9494335;

hg19: chr6-136011864;