rs1410304

Variant names:

• chr10-115622358-A-G
• rs1410304
• NM_207303.4:c.3795+72822A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-115622358-A-G
• chr10-115622358-A-T

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+72822A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,078 control chromosomes in the GnomAD database, including 18,970 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 0.48 (18970 hom., cov: 32)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.3795+72822A>G		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+72822A>G		intron_variant	Intron 26 of 28	1	NM_207303.4	ENSP00000347152.3
ATRNL1	ENST00000650603.1	n.3687+72822A>G		intron_variant	Intron 26 of 29			ENSP00000497485.1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72914 AN: 151960 Hom.: 18961 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.480 AC: 72963 AN: 152078 Hom.: 18970 Cov.: 32 AF XY: 0.492 AC XY: 36565 AN XY: 74330

African (AFR) AF: 0.304 AC: 12634 AN: 41502

American (AMR) AF: 0.588 AC: 8977 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1499 AN: 3468

East Asian (EAS) AF: 0.839 AC: 4320 AN: 5152

South Asian (SAS) AF: 0.640 AC: 3091 AN: 4826

European-Finnish (FIN) AF: 0.614 AC: 6490 AN: 10566

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34474 AN: 67970

Other (OTH) AF: 0.478 AC: 1011 AN: 2116

Alfa AF: 0.479 Hom.: 2410

Bravo AF: 0.471

Asia WGS AF: 0.692 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.58
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: rs1410304; hg19: chr10-117381868;