chr6-135788693-T-C

Variant names:

• chr6-135788693-T-C
• rs4896180
• ENST00000655302.1:n.669-21154T>C

Variant summary

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

The ENST00000655302.1(AHI1-DT):​n.669-21154T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0745 in 152,230 control chromosomes in the GnomAD database, including 687 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 0.075 (687 hom., cov: 32)
• Consequence: AHI1-DT ENST00000655302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

Genes affected

AHI1-DT (HGNC:32526): (AHI1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000655302.1	n.669-21154T>C		intron_variant	Intron 5 of 6
AHI1-DT	ENST00000685995.1	n.821+11916T>C		intron_variant	Intron 6 of 7
AHI1-DT	ENST00000690403.1	n.508-21154T>C		intron_variant	Intron 4 of 5
AHI1-DT	ENST00000702072.1	n.482-21154T>C		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11317 AN: 152112 Hom.: 685 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0508

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.0463

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.0226

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0745 AC: 11342 AN: 152230 Hom.: 687 Cov.: 32 AF XY: 0.0719 AC XY: 5353 AN XY: 74426

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0506

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.0462

Gnomad4 SAS AF: 0.0659

Gnomad4 FIN AF: 0.0226

Gnomad4 NFE AF: 0.0366

Gnomad4 OTH AF: 0.0652

Alfa AF: 0.0429 Hom.: 364

Bravo AF: 0.0824

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4896180; hg19: chr6-136109831; COSMIC: COSV69427788;