chr6-135659499-G-A

Variant names:

• chr6-135659499-G-A
• rs6935033
• ENST00000421378.4:n.283-12795G>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.283-12795G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,056 control chromosomes in the GnomAD database, including 23,353 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 0.51 (23353 hom., cov: 32)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AHI1-DT	NR_026805.1	n.285-12795G>A		intron_variant	Intron 2 of 3
AHI1-DT	NR_152842.1	n.399-12795G>A		intron_variant	Intron 3 of 5
AHI1-DT	NR_152844.1	n.399-12795G>A		intron_variant	Intron 3 of 4
AHI1-DT	NR_152845.1	n.523-12795G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000421378.4	n.283-12795G>A		intron_variant	Intron 2 of 3	1
AHI1-DT	ENST00000653664.1	n.423-12795G>A		intron_variant	Intron 3 of 4
AHI1-DT	ENST00000655302.1	n.294-12795G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77413 AN: 151938 Hom.: 23289 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.510 AC: 77533 AN: 152056 Hom.: 23353 Cov.: 32 AF XY: 0.503 AC XY: 37377 AN XY: 74316

African (AFR) AF: 0.853 AC: 35372 AN: 41490

American (AMR) AF: 0.461 AC: 7040 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1458 AN: 3460

East Asian (EAS) AF: 0.457 AC: 2365 AN: 5174

South Asian (SAS) AF: 0.507 AC: 2443 AN: 4818

European-Finnish (FIN) AF: 0.249 AC: 2635 AN: 10576

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.363 AC: 24694 AN: 67940

Other (OTH) AF: 0.497 AC: 1050 AN: 2112

Alfa AF: 0.435 Hom.: 4057

Bravo AF: 0.537

Asia WGS AF: 0.501 AC: 1740 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
DANN	Benign	0.59
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs6935033; hg19: chr6-135980637;