rs10030362

Positions:

• chr4-101701686-T-C

Variant summary

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

The XR_001741778.1(LOC107986297):​n.193+11316T>C 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 0.445 in 151,954 control chromosomes in the GnomAD database, including 15,527 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 0.45 (15527 hom., cov: 32)
• Consequence: LOC107986297 XR_001741778.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

LOC107986297 (HGNC:):

BANK1 (HGNC:18233): (B cell scaffold protein with ankyrin repeats 1) The protein encoded by this gene is a B-cell-specific scaffold protein that functions in B-cell receptor-induced calcium mobilization from intracellular stores. This protein can also promote Lyn-mediated tyrosine phosphorylation of inositol 1,4,5-trisphosphate receptors. Polymorphisms in this gene are associated with susceptibility to systemic lupus erythematosus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986297	XR_001741778.1	n.193+11316T>C		intron_variant, non_coding_transcript_variant
LOC107986297	XR_001741779.1	n.193+11316T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000504592.5	c.-45-19678T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67661 AN: 151836 Hom.: 15521 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.445 AC: 67685 AN: 151954 Hom.: 15527 Cov.: 32 AF XY: 0.435 AC XY: 32336 AN XY: 74262

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.447

Alfa AF: 0.459 Hom.: 3166

Bravo AF: 0.443

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10030362; hg19: chr4-102622843;