NM_207303.4:c.3796-7962A>C

Variant names:

• chr10-115719286-A-C
• rs10885789
• NM_207303.4:c.3796-7962A>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.3796-7962A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,906 control chromosomes in the GnomAD database, including 17,299 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 0.47 (17299 hom., cov: 32)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 0 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207303.4. 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
	ATRNL1	NM_207303.4	MANE Select	c.3796-7962A>C		intron	N/A	NP_997186.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRNL1	ENST00000355044.8	TSL:1 MANE Select	c.3796-7962A>C		intron	N/A	ENSP00000347152.3
	ATRNL1	ENST00000650603.1		n.3688-7962A>C		intron	N/A	ENSP00000497485.1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70610 AN: 151788 Hom.: 17264 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.465 AC: 70703 AN: 151906 Hom.: 17299 Cov.: 32 AF XY: 0.473 AC XY: 35144 AN XY: 74252

African (AFR) AF: 0.509 AC: 21100 AN: 41418

American (AMR) AF: 0.586 AC: 8938 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1410 AN: 3470

East Asian (EAS) AF: 0.780 AC: 4018 AN: 5150

South Asian (SAS) AF: 0.548 AC: 2643 AN: 4820

European-Finnish (FIN) AF: 0.427 AC: 4495 AN: 10536

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26599 AN: 67950

Other (OTH) AF: 0.477 AC: 1006 AN: 2108

Alfa AF: 0.304 Hom.: 801

Bravo AF: 0.481

Asia WGS AF: 0.643 AC: 2233 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.68
DANN	Benign	0.74
PhyloP100		-1.8
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: rs10885789; hg19: chr10-117478796;