rs958072

Positions:

• chr6-135506428-G-A
• chr6-135506428-G-C
• chr6-135506428-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421378.4(AHI1-DT):​n.198+8428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,128 control chromosomes in the GnomAD database, including 47,822 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 0.75 (47822 hom., cov: 32)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

Genes affected

AHI1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHI1-DT	NR_026805.1	n.200+8428G>A		intron_variant
AHI1-DT	NR_152842.1	n.314+7911G>A		intron_variant
AHI1-DT	NR_152843.1	n.314+7911G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000421378.4	n.198+8428G>A		intron_variant		1
AHI1-DT	ENST00000579339.6	n.156+7911G>A		intron_variant		1
AHI1-DT	ENST00000580741.5	n.399+6987G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113776 AN: 152010 Hom.: 47821 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.748 AC: 113807 AN: 152128 Hom.: 47822 Cov.: 32 AF XY: 0.757 AC XY: 56287 AN XY: 74388

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.956

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.768

Alfa AF: 0.761 Hom.: 6997

Bravo AF: 0.720

Asia WGS AF: 0.829 AC: 2884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs958072; hg19: chr6-135827566;