12-103856016-T-C

Variant names:

• chr12-103856016-T-C
• rs2255313
• ENST00000548520.2:n.2665+1094A>G

Variant summary

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

The ENST00000548520.2(ENSG00000293399):​n.2665+1094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,332 control chromosomes in the GnomAD database, including 69,020 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 0.95 (69020 hom., cov: 33)
• Consequence: ENSG00000293399 ENST00000548520.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 2 publications found

Genes affected

ENSG00000293399 (HGNC:):

TTC41P (HGNC:49210): (tetratricopeptide repeat domain 41, pseudogene) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC41P	NR_027249.1	n.3706+1094A>G		intron_variant	Intron 14 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293399	ENST00000548520.2	n.2665+1094A>G		intron_variant	Intron 9 of 9	5
ENSG00000293399	ENST00000548527.5	n.804+1094A>G		intron_variant	Intron 6 of 6	5
TTC41P	ENST00000551270.1	n.3160+1094A>G		intron_variant	Intron 13 of 14	6

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144817 AN: 152214 Hom.: 68963 Cov.: 33

Gnomad AFR AF: 0.985

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.951 AC: 144934 AN: 152332 Hom.: 69020 Cov.: 33 AF XY: 0.954 AC XY: 71036 AN XY: 74486

African (AFR) AF: 0.985 AC: 40936 AN: 41576

American (AMR) AF: 0.960 AC: 14685 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3362 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5194 AN: 5196

South Asian (SAS) AF: 0.982 AC: 4733 AN: 4820

European-Finnish (FIN) AF: 0.955 AC: 10144 AN: 10622

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62737 AN: 68026

Other (OTH) AF: 0.946 AC: 1997 AN: 2112

Alfa AF: 0.935 Hom.: 33400

Bravo AF: 0.954

Asia WGS AF: 0.992 AC: 3449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2255313; hg19: chr12-104249794;