rs4896180

Positions:

• chr6-135788693-T-C

Variant summary

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

The variant allele was found at a frequency of 0.0745 in 152,230 control chromosomes in the GnomAD database, including 687 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 0.075 (687 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.135788693T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000655302.1	n.669-21154T>C		intron_variant
AHI1-DT	ENST00000685995.1	n.821+11916T>C		intron_variant
AHI1-DT	ENST00000690403.1	n.508-21154T>C		intron_variant
AHI1-DT	ENST00000702072.1	n.482-21154T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11317 AN: 152112 Hom.: 685 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0508

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.0463

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.0226

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0745 AC: 11342 AN: 152230 Hom.: 687 Cov.: 32 AF XY: 0.0719 AC XY: 5353 AN XY: 74426

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0506

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.0462

Gnomad4 SAS AF: 0.0659

Gnomad4 FIN AF: 0.0226

Gnomad4 NFE AF: 0.0366

Gnomad4 OTH AF: 0.0652

Alfa AF: 0.0429 Hom.: 364

Bravo AF: 0.0824

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4896180; hg19: chr6-136109831; COSMIC: COSV69427788;