ENST00000421378.4:n.198+56807A>G

Variant names:

• chr6-135554807-A-G
• rs7752627
• ENST00000421378.4:n.198+56807A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421378.4(AHI1-DT):​n.198+56807A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,072 control chromosomes in the GnomAD database, including 10,640 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 0.26 (10640 hom., cov: 32)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 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.200+56807A>G		intron	N/A
	AHI1-DT	NR_152842.1		n.314+56290A>G		intron	N/A
	AHI1-DT	NR_152843.1		n.553-221A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000421378.4	TSL:1	n.198+56807A>G		intron	N/A
	AHI1-DT	ENST00000438618.2	TSL:3	n.146+56290A>G		intron	N/A
	AHI1-DT	ENST00000653664.1		n.338+35977A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39040 AN: 151954 Hom.: 10603 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.0964

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.257 AC: 39137 AN: 152072 Hom.: 10640 Cov.: 32 AF XY: 0.249 AC XY: 18508 AN XY: 74360

African (AFR) AF: 0.694 AC: 28749 AN: 41432

American (AMR) AF: 0.150 AC: 2284 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0599 AC: 208 AN: 3470

East Asian (EAS) AF: 0.0966 AC: 501 AN: 5186

South Asian (SAS) AF: 0.0868 AC: 419 AN: 4828

European-Finnish (FIN) AF: 0.0444 AC: 471 AN: 10612

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0873 AC: 5934 AN: 67970

Other (OTH) AF: 0.236 AC: 498 AN: 2108

Alfa AF: 0.192 Hom.: 2555

Bravo AF: 0.286

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.16
DANN	Benign	0.63
PhyloP100		-1.1

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: rs7752627;

hg19: chr6-135875945;