10-115581617-T-G

Variant names:

• chr10-115581617-T-G
• rs2769371
• NM_207303.4:c.3795+32081T>G

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+32081T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,920 control chromosomes in the GnomAD database, including 19,300 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 0.49 (19300 hom., cov: 32)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 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.3795+32081T>G		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.3795+32081T>G		intron	N/A	ENSP00000347152.3
	ATRNL1	ENST00000424738.1	TSL:3	n.379-15976T>G		intron	N/A
	ATRNL1	ENST00000650603.1		n.3687+32081T>G		intron	N/A	ENSP00000497485.1

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74208 AN: 151804 Hom.: 19285 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.489 AC: 74271 AN: 151920 Hom.: 19300 Cov.: 32 AF XY: 0.501 AC XY: 37211 AN XY: 74250

African (AFR) AF: 0.346 AC: 14327 AN: 41400

American (AMR) AF: 0.590 AC: 8997 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1489 AN: 3472

East Asian (EAS) AF: 0.839 AC: 4327 AN: 5158

South Asian (SAS) AF: 0.641 AC: 3088 AN: 4820

European-Finnish (FIN) AF: 0.613 AC: 6471 AN: 10556

Middle Eastern (MID) AF: 0.438 AC: 127 AN: 290

European-Non Finnish (NFE) AF: 0.502 AC: 34108 AN: 67950

Other (OTH) AF: 0.476 AC: 999 AN: 2100

Alfa AF: 0.490 Hom.: 2381

Bravo AF: 0.482

Asia WGS AF: 0.695 AC: 2412 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		0.30
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: rs2769371; hg19: chr10-117341127;