chr6-135753683-T-C

Variant names:

• chr6-135753683-T-C
• rs12211505
• ENST00000655302.1:n.668+37737T>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.668+37737T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,042 control chromosomes in the GnomAD database, including 11,151 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 0.37 (11151 hom., cov: 32)
• Consequence: AHI1-DT ENST00000655302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000655302.1	n.668+37737T>C		intron_variant	Intron 5 of 6
AHI1-DT	ENST00000685995.1	n.782-23055T>C		intron_variant	Intron 5 of 7
AHI1-DT	ENST00000690403.2	n.508-56164T>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55906 AN: 151924 Hom.: 11111 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.368 AC: 56001 AN: 152042 Hom.: 11151 Cov.: 32 AF XY: 0.362 AC XY: 26891 AN XY: 74364

African (AFR) AF: 0.517 AC: 21442 AN: 41452

American (AMR) AF: 0.374 AC: 5713 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1281 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2121 AN: 5166

South Asian (SAS) AF: 0.400 AC: 1927 AN: 4818

European-Finnish (FIN) AF: 0.163 AC: 1723 AN: 10590

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20583 AN: 67960

Other (OTH) AF: 0.372 AC: 784 AN: 2110

Alfa AF: 0.329 Hom.: 1812

Bravo AF: 0.389

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.74
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs12211505; hg19: chr6-136074821;