rs77803164

Positions:

• chr4-138888027-G-A

Variant summary

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

The NR_133945.1(LOC105377448):​n.162-67950C>T 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 0.0426 in 152,066 control chromosomes in the GnomAD database, including 164 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 0.043 (164 hom., cov: 31)
• Consequence: LOC105377448 NR_133945.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377448	NR_133945.1	n.162-67950C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000511951.1	n.162-67950C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000507038.1	n.159-42654C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6473 AN: 151948 Hom.: 164 Cov.: 31

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.0936

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.0583

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0202

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0606

Gnomad OTH AF: 0.0513

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

GnomAD4 genome AF: 0.0426 AC: 6474 AN: 152066 Hom.: 164 Cov.: 31 AF XY: 0.0398 AC XY: 2961 AN XY: 74320

Gnomad4 AFR AF: 0.0190

Gnomad4 AMR AF: 0.0368

Gnomad4 ASJ AF: 0.0583

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0208

Gnomad4 FIN AF: 0.0451

Gnomad4 NFE AF: 0.0606

Gnomad4 OTH AF: 0.0508

Alfa AF: 0.0525 Hom.: 34

Bravo AF: 0.0421

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77803164; hg19: chr4-139809181;