chr10-58755262-T-C

Variant names:

• chr10-58755262-T-C
• rs7094271
• NM_001080512.3:c.308-29739T>C

Variant summary

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

The NM_001080512.3(BICC1):​c.308-29739T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,938 control chromosomes in the GnomAD database, including 21,081 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 0.52 (21081 hom., cov: 32)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 4 publications found

Genes affected

BICC1 (HGNC:19351): (BicC family RNA binding protein 1) This gene encodes an RNA-binding protein that is active in regulating gene expression by modulating protein translation during embryonic development. Mouse studies identified the corresponding protein to be under strict control during cell differentiation and to be a maternally provided gene product. [provided by RefSeq, Apr 2009]

BICC1 Gene-Disease associations (from GenCC):

• renal dysplasia, cystic, susceptibility to

  Inheritance: AD, Unknown Classification: MODERATE, LIMITED Submitted by: Broad Center for Mendelian Genomics, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICC1	NM_001080512.3	c.308-29739T>C		intron_variant	Intron 3 of 20	ENST00000373886.8	NP_001073981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICC1	ENST00000373886.8	c.308-29739T>C		intron_variant	Intron 3 of 20	1	NM_001080512.3	ENSP00000362993.3

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79599 AN: 151822 Hom.: 21066 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.524 AC: 79643 AN: 151938 Hom.: 21081 Cov.: 32 AF XY: 0.520 AC XY: 38608 AN XY: 74274

African (AFR) AF: 0.469 AC: 19438 AN: 41402

American (AMR) AF: 0.625 AC: 9551 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2170 AN: 3472

East Asian (EAS) AF: 0.550 AC: 2843 AN: 5166

South Asian (SAS) AF: 0.496 AC: 2391 AN: 4822

European-Finnish (FIN) AF: 0.446 AC: 4712 AN: 10560

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36664 AN: 67932

Other (OTH) AF: 0.532 AC: 1122 AN: 2110

Alfa AF: 0.528 Hom.: 16702

Bravo AF: 0.539

Asia WGS AF: 0.514 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.56
DANN	Benign	0.50
PhyloP100		-0.18
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: rs7094271; hg19: chr10-60515022;