chr6-135615740-G-A

Position:

• chr6-135615740-G-A

Variant summary

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

The NR_152842.1(AHI1-DT):​n.315-26453G>A 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 0.461 in 152,062 control chromosomes in the GnomAD database, including 17,869 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 0.46 (17869 hom., cov: 31)
• Consequence: AHI1-DT NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1-DT	NR_152842.1	n.315-26453G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_026805.1	n.201-26453G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152844.1	n.315-26453G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152845.1	n.439-26453G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.148-26453G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69966 AN: 151944 Hom.: 17830 Cov.: 31

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.461 AC: 70060 AN: 152062 Hom.: 17869 Cov.: 31 AF XY: 0.454 AC XY: 33716 AN XY: 74338

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.437

Alfa AF: 0.280 Hom.: 666

Bravo AF: 0.473

Asia WGS AF: 0.399 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.65
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6925684; hg19: chr6-135936878;