10-115729768-T-C

Variant names:

• chr10-115729768-T-C
• rs2804161
• NM_207303.4:c.3903+2413T>C

Variant summary

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

The NM_207303.4(ATRNL1):​c.3903+2413T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,954 control chromosomes in the GnomAD database, including 11,878 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 (11878 hom., cov: 31)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 1 publications found

Genes affected

ATRNL1 (HGNC:29063): (attractin like 1) Predicted to enable carbohydrate binding activity. Predicted to be involved in several processes, including animal organ morphogenesis; cell migration; and substrate adhesion-dependent cell spreading. Predicted to act upstream of or within G protein-coupled receptor signaling pathway. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in basement membrane. [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 (NFE) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.3903+2413T>C		intron_variant	Intron 27 of 28	ENST00000355044.8	NP_997186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATRNL1	ENST00000355044.8	c.3903+2413T>C		intron_variant	Intron 27 of 28	1	NM_207303.4	ENSP00000347152.3
ATRNL1	ENST00000650603.1	n.3795+2413T>C		intron_variant	Intron 27 of 29			ENSP00000497485.1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56446 AN: 151838 Hom.: 11882 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.372 AC: 56453 AN: 151954 Hom.: 11878 Cov.: 31 AF XY: 0.372 AC XY: 27603 AN XY: 74274

African (AFR) AF: 0.174 AC: 7205 AN: 41468

American (AMR) AF: 0.345 AC: 5270 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1424 AN: 3466

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5162

South Asian (SAS) AF: 0.477 AC: 2297 AN: 4812

European-Finnish (FIN) AF: 0.473 AC: 4977 AN: 10520

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32637 AN: 67948

Other (OTH) AF: 0.372 AC: 784 AN: 2106

Alfa AF: 0.438 Hom.: 22107

Bravo AF: 0.351

Asia WGS AF: 0.353 AC: 1226 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	1.9
DANN	Benign	0.67
PhyloP100		-0.55
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: rs2804161; hg19: chr10-117489278;