rs2507971

Variant names:

• chr6-31493595-A-T
• rs2507971
• ENST00000656299.1:n.67+659T>A

Variant summary

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

The NR_149132.1(MICB-DT):​n.541+659T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,948 control chromosomes in the GnomAD database, including 27,273 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 0.60 (27273 hom., cov: 32)
• Consequence: MICB-DT NR_149132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 6 publications found

Genes affected

MICB-DT (HGNC:53632): (MICB divergent transcript)

HCP5 (HGNC:21659): (HLA complex P5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_149132.1. 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
	MICB-DT	NR_149132.1		n.541+659T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	ENST00000656299.1		n.67+659T>A		intron	N/A
	MICB-DT	ENST00000665353.2		n.682+659T>A		intron	N/A
	HCP5	ENST00000718214.1		n.156-663A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90393 AN: 151828 Hom.: 27252 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.595 AC: 90453 AN: 151948 Hom.: 27273 Cov.: 32 AF XY: 0.594 AC XY: 44095 AN XY: 74264

African (AFR) AF: 0.543 AC: 22497 AN: 41394

American (AMR) AF: 0.648 AC: 9892 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2426 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3823 AN: 5178

South Asian (SAS) AF: 0.621 AC: 2993 AN: 4816

European-Finnish (FIN) AF: 0.498 AC: 5239 AN: 10526

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41546 AN: 67974

Other (OTH) AF: 0.573 AC: 1208 AN: 2110

Alfa AF: 0.599 Hom.: 3440

Bravo AF: 0.608

Asia WGS AF: 0.616 AC: 2146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.53
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2507971; hg19: chr6-31461372;