chr10-115437655-T-C

Variant names:

• chr10-115437655-T-C
• rs585354
• NM_207303.4:c.3322+11353T>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.3322+11353T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,028 control chromosomes in the GnomAD database, including 2,662 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 0.10 (2662 hom., cov: 32)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.3322+11353T>C		intron_variant	Intron 21 of 28	ENST00000355044.8	NP_997186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATRNL1	ENST00000355044.8	c.3322+11353T>C		intron_variant	Intron 21 of 28	1	NM_207303.4	ENSP00000347152.3
ATRNL1	ENST00000526373.1	c.571+11353T>C		intron_variant	Intron 5 of 5	5		ENSP00000434118.1
ATRNL1	ENST00000534530.5	n.437+11353T>C		intron_variant	Intron 4 of 5	4
ATRNL1	ENST00000650603.1	n.3214+11353T>C		intron_variant	Intron 21 of 29			ENSP00000497485.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15592 AN: 151910 Hom.: 2651 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0448

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.00140

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.103 AC: 15632 AN: 152028 Hom.: 2662 Cov.: 32 AF XY: 0.0987 AC XY: 7334 AN XY: 74322

African (AFR) AF: 0.353 AC: 14650 AN: 41464

American (AMR) AF: 0.0446 AC: 681 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4824

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10622

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.00140 AC: 95 AN: 67874

Other (OTH) AF: 0.0710 AC: 150 AN: 2112

Alfa AF: 0.0155 Hom.: 55

Bravo AF: 0.119

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.72
PhyloP100		-0.024
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: rs585354; hg19: chr10-117197165;