rs10517377

Positions:

• chr4-36267390-A-C
• chr4-36267390-A-G
• chr4-36267390-A-T

Variant summary

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

The NR_122079.1(LOC439933):​n.361-5557A>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 0.18 in 152,214 control chromosomes in the GnomAD database, including 2,993 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 0.18 (2993 hom., cov: 32)
• Consequence: LOC439933 NR_122079.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC439933	NR_122079.1	n.361-5557A>C		intron_variant, non_coding_transcript_variant
LOC439933	NR_122080.1	n.338-5845A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000499292.2	n.361-5557A>C		intron_variant, non_coding_transcript_variant		1
	ENST00000502245.2	n.386-5845A>C		intron_variant, non_coding_transcript_variant		1
	ENST00000691596.1	n.193-5845A>C		intron_variant, non_coding_transcript_variant
	ENST00000692213.1	n.193-5557A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27428 AN: 152096 Hom.: 2992 Cov.: 32

Gnomad AFR AF: 0.0674

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0758

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.180 AC: 27428 AN: 152214 Hom.: 2993 Cov.: 32 AF XY: 0.178 AC XY: 13241 AN XY: 74404

Gnomad4 AFR AF: 0.0673

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.0762

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.191

Alfa AF: 0.130 Hom.: 292

Bravo AF: 0.176

Asia WGS AF: 0.141 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.28
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517377; hg19: chr4-36269012;