4-74357994-A-G

Variant names:

• chr4-74357994-A-G
• rs2168889
• ENST00000805841.1:n.191+7157T>C

Variant summary

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

The NR_188415.1(LOC105377276):​n.191+7157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0471 in 152,198 control chromosomes in the GnomAD database, including 185 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 0.047 (185 hom., cov: 32)
• Consequence: LOC105377276 NR_188415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637
• Publications: 9 publications found

Genes affected

ENSG00000304732 (HGNC:58817):

LOC105377276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188415.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105377276	NR_188415.1		n.191+7157T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304732	ENST00000805841.1		n.191+7157T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7171 AN: 152080 Hom.: 184 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0281

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.0513

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0450

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0471 AC: 7166 AN: 152198 Hom.: 185 Cov.: 32 AF XY: 0.0478 AC XY: 3559 AN XY: 74402

African (AFR) AF: 0.0479 AC: 1988 AN: 41538

American (AMR) AF: 0.0281 AC: 429 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3470

East Asian (EAS) AF: 0.0945 AC: 490 AN: 5184

South Asian (SAS) AF: 0.0645 AC: 311 AN: 4824

European-Finnish (FIN) AF: 0.0513 AC: 543 AN: 10590

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0451 AC: 3063 AN: 67986

Other (OTH) AF: 0.0379 AC: 80 AN: 2110

Alfa AF: 0.0483 Hom.: 315

Bravo AF: 0.0454

Asia WGS AF: 0.0710 AC: 245 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.75
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs2168889; hg19: chr4-75223711;