rs1316981

chr1-51569386-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_161259.1(CALR4P):n.684+162A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,064 control chromosomes in the GnomAD database, including 5,191 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 0.24 (5191 hom., cov: 32)
• Consequence: CALR4P NR_161259.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

Genes affected

CALR4P (HGNC:35456): (calreticulin 4, pseudogene)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CALR4P	NR_161259.1	n.684+162A>G		intron_variant, non_coding_transcript_variant
EPS15-AS1	NR_183651.1	n.318-4607T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALR4P	ENST00000431943.1	n.336+162A>G		intron_variant, non_coding_transcript_variant
	ENST00000641477.1	n.680+162A>G		intron_variant, non_coding_transcript_variant
	ENST00000641070.1	n.598+162A>G		intron_variant, non_coding_transcript_variant
	ENST00000641201.1	n.709+162A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36189 AN: 151944 Hom.: 5189 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.238 AC: 36186 AN: 152064 Hom.: 5191 Cov.: 32 AF XY: 0.233 AC XY: 17317 AN XY: 74332

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.287

Alfa AF: 0.314 Hom.: 8705

Bravo AF: 0.230

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.0
Dann	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1316981; hg19: chr1-52035058;