rs4896180

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655302.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000655302.1		n.669-21154T>C		intron	N/A
	AHI1-DT	ENST00000685995.1		n.821+11916T>C		intron	N/A
	AHI1-DT	ENST00000690403.2		n.508-21154T>C		intron	N/A

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

African (AFR) AF: 0.171 AC: 7095 AN: 41542

American (AMR) AF: 0.0506 AC: 772 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3468

East Asian (EAS) AF: 0.0462 AC: 240 AN: 5192

South Asian (SAS) AF: 0.0659 AC: 318 AN: 4826

European-Finnish (FIN) AF: 0.0226 AC: 240 AN: 10624

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.0366 AC: 2487 AN: 67988

Other (OTH) AF: 0.0652 AC: 138 AN: 2116

Alfa AF: 0.0495 Hom.: 847

Bravo AF: 0.0824

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.76
PhyloP100		-0.21

Splicing

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

Other links and lift over

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