ENST00000421378.4:n.418+4211C>T

Variant names:

• chr6-135676640-C-T
• rs7739635
• ENST00000421378.4:n.418+4211C>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.418+4211C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,994 control chromosomes in the GnomAD database, including 22,524 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 0.50 (22524 hom., cov: 31)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AHI1-DT	NR_026805.1	n.420+4211C>T		intron_variant	Intron 3 of 3
AHI1-DT	NR_152842.1	n.534+4211C>T		intron_variant	Intron 4 of 5
AHI1-DT	NR_152844.1	n.534+4211C>T		intron_variant	Intron 4 of 4
AHI1-DT	NR_152845.1	n.658+4211C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000421378.4	n.418+4211C>T		intron_variant	Intron 3 of 3	1
AHI1-DT	ENST00000579944.1	n.116+4211C>T		intron_variant	Intron 1 of 2	2
AHI1-DT	ENST00000653664.1	n.558+4211C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75939 AN: 151876 Hom.: 22464 Cov.: 31

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.500 AC: 76057 AN: 151994 Hom.: 22524 Cov.: 31 AF XY: 0.491 AC XY: 36497 AN XY: 74278

African (AFR) AF: 0.834 AC: 34597 AN: 41482

American (AMR) AF: 0.459 AC: 6998 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1469 AN: 3460

East Asian (EAS) AF: 0.454 AC: 2343 AN: 5158

South Asian (SAS) AF: 0.505 AC: 2431 AN: 4816

European-Finnish (FIN) AF: 0.204 AC: 2156 AN: 10564

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24553 AN: 67948

Other (OTH) AF: 0.492 AC: 1039 AN: 2110

Alfa AF: 0.410 Hom.: 7616

Bravo AF: 0.531

Asia WGS AF: 0.504 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.51
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs7739635; hg19: chr6-135997778;