rs2143681

Variant names:

• chr6-135611867-G-A
• rs2143681
• ENST00000421378.4:n.199-30326G>A

Variant summary

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

The ENST00000421378.4(AHI1-DT):​n.199-30326G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 152,004 control chromosomes in the GnomAD database, including 17,856 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 0.46 (17856 hom., cov: 32)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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.201-30326G>A		intron	N/A
	AHI1-DT	NR_152842.1		n.315-30326G>A		intron	N/A
	AHI1-DT	NR_152844.1		n.315-30326G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000421378.4	TSL:1	n.199-30326G>A		intron	N/A
	AHI1-DT	ENST00000438618.2	TSL:3	n.147-19744G>A		intron	N/A
	AHI1-DT	ENST00000653664.1		n.339-30326G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69949 AN: 151888 Hom.: 17818 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.435

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.461 AC: 70041 AN: 152004 Hom.: 17856 Cov.: 32 AF XY: 0.454 AC XY: 33707 AN XY: 74304

African (AFR) AF: 0.705 AC: 29213 AN: 41454

American (AMR) AF: 0.353 AC: 5398 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1268 AN: 3466

East Asian (EAS) AF: 0.307 AC: 1589 AN: 5182

South Asian (SAS) AF: 0.450 AC: 2169 AN: 4820

European-Finnish (FIN) AF: 0.294 AC: 3102 AN: 10566

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25963 AN: 67918

Other (OTH) AF: 0.437 AC: 923 AN: 2112

Alfa AF: 0.410 Hom.: 37274

Bravo AF: 0.473

Asia WGS AF: 0.400 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.34
PhyloP100		-0.28

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: rs2143681;

hg19: chr6-135933005;