1-174854701-A-T

Variant names:

• chr1-174854701-A-T
• rs1231828
• NM_001366446.1:c.2340+42741A>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001366446.1(RABGAP1L):​c.2340+42741A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 25)
  • Failed GnomAD Quality Control
• Consequence: RABGAP1L NM_001366446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 0 publications found

Genes affected

RABGAP1L (HGNC:24663): (RAB GTPase activating protein 1 like) Enables GTPase activator activity and small GTPase binding activity. Acts upstream of or within regulation of protein localization. Located in Golgi apparatus; early endosome; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RABGAP1L	NM_001366446.1	MANE Select	c.2340+42741A>T		intron	N/A	NP_001353375.1	A0A804HKD7
	RABGAP1L	NM_001366448.1		c.2340+42741A>T		intron	N/A	NP_001353377.1
	RABGAP1L	NM_014857.5		c.2340+42741A>T		intron	N/A	NP_055672.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RABGAP1L	ENST00000681986.1	MANE Select	c.2340+42741A>T		intron	N/A	ENSP00000507884.1	A0A804HKD7
	RABGAP1L	ENST00000347255.6	TSL:1	c.321+42741A>T		intron	N/A	ENSP00000281844.5	Q5R372-5
	RABGAP1L	ENST00000489615.5	TSL:1	c.297+42741A>T		intron	N/A	ENSP00000420660.1	Q5R372-8

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 132632 Hom.: 0 Cov.: 25

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 132632 Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0 AN XY: 63378

African (AFR) AF: 0.00 AC: 0 AN: 36230

American (AMR) AF: 0.00 AC: 0 AN: 12602

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3218

East Asian (EAS) AF: 0.00 AC: 0 AN: 4750

South Asian (SAS) AF: 0.00 AC: 0 AN: 4040

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6558

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 244

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 62354

Other (OTH) AF: 0.00 AC: 0 AN: 1796

Alfa AF: 0.00 Hom.: 334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.43
PhyloP100		-0.19

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: rs1231828; hg19: chr1-174823839;