chr6-135738039-G-T

Position:

• chr6-135738039-G-T

Variant summary

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

The ENST00000702072.1(AHI1-DT):​n.481+48303G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,108 control chromosomes in the GnomAD database, including 5,775 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 (5775 hom., cov: 32)
• Consequence: AHI1-DT ENST00000702072.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.481+48303G>T		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000655302.1	n.668+22093G>T		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000685995.1	n.782-38699G>T		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000690403.1	n.507+48303G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39044 AN: 151988 Hom.: 5764 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.257 AC: 39072 AN: 152108 Hom.: 5775 Cov.: 32 AF XY: 0.254 AC XY: 18865 AN XY: 74366

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.264

Alfa AF: 0.299 Hom.: 9414

Bravo AF: 0.262

Asia WGS AF: 0.397 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.71
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2038551; hg19: chr6-136059177;