6-135606862-A-C

Variant names:

• chr6-135606862-A-C
• rs9376112
• ENST00000421378.4:n.199-35331A>C

Variant summary

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

The ENST00000421378.4(AHI1-DT):​n.199-35331A>C 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 152,032 control chromosomes in the GnomAD database, including 17,945 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 (17945 hom., cov: 33)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AHI1-DT	NR_026805.1	n.201-35331A>C		intron_variant	Intron 1 of 3
AHI1-DT	NR_152842.1	n.315-35331A>C		intron_variant	Intron 2 of 5
AHI1-DT	NR_152844.1	n.315-35331A>C		intron_variant	Intron 2 of 4
AHI1-DT	NR_152845.1	n.439-35331A>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000421378.4	n.199-35331A>C		intron_variant	Intron 1 of 3	1
AHI1-DT	ENST00000438618.2	n.147-24749A>C		intron_variant	Intron 2 of 4	3
AHI1-DT	ENST00000653664.1	n.339-35331A>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70028 AN: 151914 Hom.: 17905 Cov.: 33

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.461 AC: 70123 AN: 152032 Hom.: 17945 Cov.: 33 AF XY: 0.454 AC XY: 33723 AN XY: 74314

African (AFR) AF: 0.709 AC: 29361 AN: 41434

American (AMR) AF: 0.354 AC: 5413 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1179 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1589 AN: 5176

South Asian (SAS) AF: 0.451 AC: 2174 AN: 4820

European-Finnish (FIN) AF: 0.295 AC: 3116 AN: 10564

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25956 AN: 67970

Other (OTH) AF: 0.435 AC: 918 AN: 2110

Alfa AF: 0.426 Hom.: 1833

Bravo AF: 0.474

Asia WGS AF: 0.400 AC: 1392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.75
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9376112; hg19: chr6-135928000;