6-135576797-C-T

Variant names:

• chr6-135576797-C-T
• rs10484771
• ENST00000421378.4:n.199-65396C>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.199-65396C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0544 in 152,198 control chromosomes in the GnomAD database, including 425 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 0.054 (425 hom., cov: 32)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 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.201-65396C>T		intron	N/A
	AHI1-DT	NR_152842.1		n.315-65396C>T		intron	N/A
	AHI1-DT	NR_152844.1		n.315-65396C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000421378.4	TSL:1	n.199-65396C>T		intron	N/A
	AHI1-DT	ENST00000438618.2	TSL:3	n.147-54814C>T		intron	N/A
	AHI1-DT	ENST00000653664.1		n.338+57967C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0545 AC: 8287 AN: 152080 Hom.: 425 Cov.: 32

Gnomad AFR AF: 0.00975

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0583

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.0617

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0544 AC: 8282 AN: 152198 Hom.: 425 Cov.: 32 AF XY: 0.0581 AC XY: 4325 AN XY: 74424

African (AFR) AF: 0.00972 AC: 404 AN: 41568

American (AMR) AF: 0.0377 AC: 576 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0583 AC: 202 AN: 3464

East Asian (EAS) AF: 0.254 AC: 1311 AN: 5168

South Asian (SAS) AF: 0.0616 AC: 297 AN: 4822

European-Finnish (FIN) AF: 0.129 AC: 1371 AN: 10602

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0577 AC: 3919 AN: 67974

Other (OTH) AF: 0.0587 AC: 124 AN: 2112

Alfa AF: 0.0559 Hom.: 460

Bravo AF: 0.0471

Asia WGS AF: 0.110 AC: 382 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.7
DANN	Benign	0.59
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

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: rs10484771;

hg19: chr6-135897935;