10-115565511-T-C

Variant names:

• chr10-115565511-T-C
• rs1572396
• NM_207303.4:c.3795+15975T>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.3795+15975T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,774 control chromosomes in the GnomAD database, including 26,841 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 0.57 (26841 hom., cov: 31)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.3795+15975T>C		intron_variant	Intron 26 of 28	ENST00000355044.8	NP_997186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATRNL1	ENST00000355044.8	c.3795+15975T>C		intron_variant	Intron 26 of 28	1	NM_207303.4	ENSP00000347152.3
ATRNL1	ENST00000424738.1	n.378+15975T>C		intron_variant	Intron 4 of 4	3
ATRNL1	ENST00000650603.1	n.3687+15975T>C		intron_variant	Intron 26 of 29			ENSP00000497485.1

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87076 AN: 151656 Hom.: 26838 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.574 AC: 87093 AN: 151774 Hom.: 26841 Cov.: 31 AF XY: 0.565 AC XY: 41921 AN XY: 74160

African (AFR) AF: 0.413 AC: 17093 AN: 41408

American (AMR) AF: 0.491 AC: 7465 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2550 AN: 3460

East Asian (EAS) AF: 0.202 AC: 1040 AN: 5154

South Asian (SAS) AF: 0.544 AC: 2622 AN: 4820

European-Finnish (FIN) AF: 0.570 AC: 6011 AN: 10546

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48078 AN: 67856

Other (OTH) AF: 0.629 AC: 1325 AN: 2106

Alfa AF: 0.667 Hom.: 17685

Bravo AF: 0.554

Asia WGS AF: 0.363 AC: 1265 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	0.55
DANN	Benign	0.41
PhyloP100		-1.1
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: rs1572396; hg19: chr10-117325021;