chr1-178546177-G-A

Variant names:

• chr1-178546177-G-A
• rs4650994
• ENST00000419909.6:n.*1113-917G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419909.6(TEX35):​n.*1113-917G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,924 control chromosomes in the GnomAD database, including 14,017 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 0.41 (14017 hom., cov: 31)
• Consequence: TEX35 ENST00000419909.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 66 publications found

Genes affected

TEX35 (HGNC:25366): (testis expressed 35) Located in microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

C1orf220 (HGNC:33805): (chromosome 1 putative open reading frame 220)

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 (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419909.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf220	NR_033186.1		n.781+274G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX35	ENST00000419909.6	TSL:2	n.*1113-917G>A		intron	N/A	ENSP00000430720.1
	C1orf220	ENST00000521244.1	TSL:2	n.781+274G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61795 AN: 151804 Hom.: 14022 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.407 AC: 61787 AN: 151924 Hom.: 14017 Cov.: 31 AF XY: 0.403 AC XY: 29923 AN XY: 74214

African (AFR) AF: 0.188 AC: 7801 AN: 41464

American (AMR) AF: 0.391 AC: 5967 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1667 AN: 3464

East Asian (EAS) AF: 0.532 AC: 2738 AN: 5148

South Asian (SAS) AF: 0.498 AC: 2395 AN: 4806

European-Finnish (FIN) AF: 0.443 AC: 4666 AN: 10536

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35231 AN: 67924

Other (OTH) AF: 0.407 AC: 859 AN: 2112

Alfa AF: 0.480 Hom.: 72749

Bravo AF: 0.389

Asia WGS AF: 0.505 AC: 1756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.57
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4650994; hg19: chr1-178515312;