1-207649816-T-C

Position:

• chr1-207649816-T-C

Variant summary

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

The NM_175710.2(CR1L):​c.97+4486T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,000 control chromosomes in the GnomAD database, including 11,720 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 0.39 (11720 hom., cov: 31)
• Consequence: CR1L NM_175710.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

Genes affected

CR1L (HGNC:2335): (complement C3b/C4b receptor 1 like) Acts upstream of or within regulation of complement activation and regulation of complement-dependent cytotoxicity. Part of receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

CD46P1 (HGNC:6959): (CD46 molecule pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CR1L	NM_175710.2	c.97+4486T>C		intron_variant		ENST00000508064.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CR1L	ENST00000508064.7	c.97+4486T>C		intron_variant		1	NM_175710.2	P1
CD46P1	ENST00000441364.1	n.98-2731T>C		intron_variant, non_coding_transcript_variant
CR1L	ENST00000531844.5	n.218+4486T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59194 AN: 151882 Hom.: 11714 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.390 AC: 59236 AN: 152000 Hom.: 11720 Cov.: 31 AF XY: 0.384 AC XY: 28550 AN XY: 74288

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.381

Alfa AF: 0.382 Hom.: 7503

Bravo AF: 0.393

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs1323720; hg19: chr1-207823161; COSMIC: COSV71558113;