rs6503448

Variant names:

• chr17-45765107-G-A
• rs6503448
• ENST00000634540.1:c.-492-41903G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-45765107-G-A
• chr17-45765107-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634540.1(LINC02210-CRHR1):​c.-492-41903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,082 control chromosomes in the GnomAD database, including 27,597 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 0.58 (27597 hom., cov: 33)
• Consequence: LINC02210-CRHR1 ENST00000634540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 8 publications found

Genes affected

LINC02210-CRHR1 (HGNC:51483): (LINC02210-CRHR1 readthrough) This locus represents naturally occurring readthrough transcription between neighboring genes CRHR1-IT1, CRHR1 intronic transcript 1 (Gene ID: 147081) and CRHR1, corticotropin releasing hormone receptor 1 (Gene ID: 1394) on chromosome 17. The readthrough transcript encodes a protein that shares sequence identity with the product of the CRHR1 gene. [provided by RefSeq, Dec 2016]

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 = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001303016.1	c.-184-41903G>A		intron_variant	Intron 3 of 12		NP_001289945.1
LINC02210-CRHR1	NM_001256299.3	c.-492-41903G>A		intron_variant	Intron 3 of 14		NP_001243228.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02210-CRHR1	ENST00000634540.1	c.-492-41903G>A		intron_variant	Intron 3 of 14	2		ENSP00000488912.1
LINC02210-CRHR1	ENST00000587305.1	n.448-41903G>A		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88570 AN: 151964 Hom.: 27562 Cov.: 33

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.583 AC: 88656 AN: 152082 Hom.: 27597 Cov.: 33 AF XY: 0.566 AC XY: 42054 AN XY: 74340

African (AFR) AF: 0.773 AC: 32099 AN: 41514

American (AMR) AF: 0.510 AC: 7792 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2017 AN: 3466

East Asian (EAS) AF: 0.148 AC: 765 AN: 5178

South Asian (SAS) AF: 0.313 AC: 1511 AN: 4832

European-Finnish (FIN) AF: 0.372 AC: 3933 AN: 10572

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38663 AN: 67924

Other (OTH) AF: 0.578 AC: 1222 AN: 2114

Alfa AF: 0.566 Hom.: 40470

Bravo AF: 0.604

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.9
DANN	Benign	0.58
PhyloP100		-0.21
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: rs6503448; hg19: chr17-43842473;