10-58756575-C-T

Variant names:

• chr10-58756575-C-T
• rs11815410
• NM_001080512.3:c.308-28426C>T

Variant summary

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

The NM_001080512.3(BICC1):​c.308-28426C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,036 control chromosomes in the GnomAD database, including 12,718 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 0.40 (12718 hom., cov: 30)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080512.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICC1	NM_001080512.3	MANE Select	c.308-28426C>T		intron	N/A	NP_001073981.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICC1	ENST00000373886.8	TSL:1 MANE Select	c.308-28426C>T		intron	N/A	ENSP00000362993.3

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59691 AN: 150930 Hom.: 12709 Cov.: 30

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.395 AC: 59713 AN: 151036 Hom.: 12718 Cov.: 30 AF XY: 0.398 AC XY: 29345 AN XY: 73720

African (AFR) AF: 0.227 AC: 9293 AN: 40944

American (AMR) AF: 0.542 AC: 8227 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1587 AN: 3468

East Asian (EAS) AF: 0.520 AC: 2679 AN: 5150

South Asian (SAS) AF: 0.472 AC: 2260 AN: 4790

European-Finnish (FIN) AF: 0.408 AC: 4221 AN: 10358

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.441 AC: 29906 AN: 67836

Other (OTH) AF: 0.418 AC: 880 AN: 2104

Alfa AF: 0.441 Hom.: 21707

Bravo AF: 0.400

Asia WGS AF: 0.468 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.87
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: rs11815410; hg19: chr10-60516335;