10-115917623-T-C

Variant names:

• chr10-115917623-T-C
• rs17354968
• NM_207303.4:c.4019-27035T>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.4019-27035T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,170 control chromosomes in the GnomAD database, including 2,392 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 0.16 (2392 hom., cov: 32)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 3 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]

ENSG00000300703 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.4019-27035T>C		intron_variant	Intron 28 of 28	ENST00000355044.8	NP_997186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATRNL1	ENST00000355044.8	c.4019-27035T>C		intron_variant	Intron 28 of 28	1	NM_207303.4	ENSP00000347152.3
ATRNL1	ENST00000449616.2	n.227+8046T>C		intron_variant	Intron 1 of 1	4
ATRNL1	ENST00000650603.1	n.3911-13905T>C		intron_variant	Intron 28 of 29			ENSP00000497485.1
ENSG00000300703	ENST00000773520.1	n.72+1460A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24830 AN: 152052 Hom.: 2399 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0412

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.163 AC: 24819 AN: 152170 Hom.: 2392 Cov.: 32 AF XY: 0.161 AC XY: 11945 AN XY: 74380

African (AFR) AF: 0.0700 AC: 2908 AN: 41544

American (AMR) AF: 0.158 AC: 2409 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3470

East Asian (EAS) AF: 0.0411 AC: 213 AN: 5180

South Asian (SAS) AF: 0.174 AC: 841 AN: 4820

European-Finnish (FIN) AF: 0.186 AC: 1962 AN: 10564

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15137 AN: 67990

Other (OTH) AF: 0.167 AC: 352 AN: 2114

Alfa AF: 0.178 Hom.: 428

Bravo AF: 0.157

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.5
DANN	Benign	0.82
PhyloP100		-0.045
Mutation Taster		=99/1	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: rs17354968; hg19: chr10-117677134;